Starting phenix.real_space_refine on Mon Aug 25 20:36:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wv6_37866/08_2025/8wv6_37866.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wv6_37866/08_2025/8wv6_37866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wv6_37866/08_2025/8wv6_37866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wv6_37866/08_2025/8wv6_37866.map" model { file = "/net/cci-nas-00/data/ceres_data/8wv6_37866/08_2025/8wv6_37866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wv6_37866/08_2025/8wv6_37866.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 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: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 19374 2.51 5 N 5442 2.21 5 O 6018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30984 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5116 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Conformer: "B" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} bond proxies already assigned to first conformer: 5202 Chain: "B" Number of atoms: 5116 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Conformer: "B" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} bond proxies already assigned to first conformer: 5202 Chain: "E" Number of atoms: 5116 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Conformer: "B" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} bond proxies already assigned to first conformer: 5202 Chain: "G" Number of atoms: 5116 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Conformer: "B" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} bond proxies already assigned to first conformer: 5202 Chain: "I" Number of atoms: 5116 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Conformer: "B" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} bond proxies already assigned to first conformer: 5202 Chain: "K" Number of atoms: 5116 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Conformer: "B" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} bond proxies already assigned to first conformer: 5202 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "G" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "I" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Time building chain proxies: 10.95, per 1000 atoms: 0.35 Number of scatterers: 30984 At special positions: 0 Unit cell: (170.13, 180.83, 110.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 150 16.00 O 6018 8.00 N 5442 7.00 C 19374 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: 2.45 Conformation dependent library (CDL) restraints added in 2.7 seconds Enol-peptide restraints added in 476.8 nanoseconds 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7416 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 33 sheets defined 43.1% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 40 through 51 Processing helix chain 'A' and resid 51 through 59 removed outlier: 3.697A pdb=" N ALA A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 78 removed outlier: 3.627A pdb=" N GLU A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 88 removed outlier: 3.976A pdb=" N PHE A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 118 Processing helix chain 'A' and resid 161 through 175 removed outlier: 4.027A pdb=" N LYS A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 186 through 200 removed outlier: 4.054A pdb=" N THR A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 192 " --> pdb=" O GLN A 188 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 233 through 242 removed outlier: 3.648A pdb=" N VAL A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 273 through 289 removed outlier: 3.884A pdb=" N ALA A 277 " --> pdb=" O GLN A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 292 No H-bonds generated for 'chain 'A' and resid 290 through 292' Processing helix chain 'A' and resid 307 through 321 removed outlier: 3.891A pdb=" N LYS A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 356 Processing helix chain 'A' and resid 384 through 393 removed outlier: 3.849A pdb=" N GLU A 387 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR A 388 " --> pdb=" O PRO A 385 " (cutoff:3.500A) Proline residue: A 389 - end of helix Processing helix chain 'A' and resid 410 through 418 Processing helix chain 'A' and resid 431 through 443 Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.703A pdb=" N LYS A 458 " --> pdb=" O GLU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 486 through 492 removed outlier: 4.001A pdb=" N VAL A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 525 through 529 Processing helix chain 'A' and resid 530 through 534 Processing helix chain 'A' and resid 548 through 560 Processing helix chain 'A' and resid 563 through 568 Processing helix chain 'A' and resid 568 through 574 removed outlier: 3.748A pdb=" N GLU A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 596 Processing helix chain 'B' and resid 40 through 51 removed outlier: 3.546A pdb=" N LYS B 51 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 59 removed outlier: 3.591A pdb=" N ALA B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 78 removed outlier: 3.612A pdb=" N GLU B 78 " --> pdb=" O HIS B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 87 removed outlier: 4.020A pdb=" N PHE B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 92 through 118 Processing helix chain 'B' and resid 161 through 174 removed outlier: 4.294A pdb=" N LYS B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 186 through 201 removed outlier: 4.048A pdb=" N THR B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 192 " --> pdb=" O GLN B 188 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY B 201 " --> pdb=" O ILE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 removed outlier: 3.611A pdb=" N LEU B 222 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 242 removed outlier: 3.523A pdb=" N VAL B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 273 through 289 removed outlier: 3.812A pdb=" N ALA B 277 " --> pdb=" O GLN B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 293 Processing helix chain 'B' and resid 307 through 321 removed outlier: 3.769A pdb=" N LYS B 321 " --> pdb=" O ALA B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 356 Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.594A pdb=" N GLU B 387 " --> pdb=" O GLN B 384 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR B 388 " --> pdb=" O PRO B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 410 through 418 Processing helix chain 'B' and resid 431 through 443 Processing helix chain 'B' and resid 455 through 459 removed outlier: 3.779A pdb=" N LYS B 458 " --> pdb=" O GLU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 486 through 491 removed outlier: 3.982A pdb=" N VAL B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 511 Processing helix chain 'B' and resid 525 through 529 Processing helix chain 'B' and resid 548 through 560 Processing helix chain 'B' and resid 563 through 568 Processing helix chain 'B' and resid 568 through 574 removed outlier: 3.636A pdb=" N GLU B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 596 Processing helix chain 'E' and resid 40 through 58 removed outlier: 4.128A pdb=" N ALA E 53 " --> pdb=" O ILE E 49 " (cutoff:3.500A) Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 60 through 78 removed outlier: 3.635A pdb=" N GLU E 78 " --> pdb=" O HIS E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 88 removed outlier: 4.034A pdb=" N PHE E 82 " --> pdb=" O GLU E 78 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN E 88 " --> pdb=" O ALA E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 118 Processing helix chain 'E' and resid 161 through 174 removed outlier: 4.209A pdb=" N LYS E 167 " --> pdb=" O GLY E 163 " (cutoff:3.500A) Proline residue: E 170 - end of helix Processing helix chain 'E' and resid 183 through 185 No H-bonds generated for 'chain 'E' and resid 183 through 185' Processing helix chain 'E' and resid 186 through 201 removed outlier: 4.094A pdb=" N THR E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY E 201 " --> pdb=" O ILE E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 222 removed outlier: 3.774A pdb=" N LEU E 222 " --> pdb=" O LEU E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 242 removed outlier: 3.676A pdb=" N VAL E 242 " --> pdb=" O GLN E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 249 Processing helix chain 'E' and resid 273 through 289 removed outlier: 3.838A pdb=" N ALA E 277 " --> pdb=" O GLN E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 293 Processing helix chain 'E' and resid 307 through 321 removed outlier: 3.784A pdb=" N LYS E 321 " --> pdb=" O ALA E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 356 Processing helix chain 'E' and resid 384 through 393 removed outlier: 3.534A pdb=" N GLU E 387 " --> pdb=" O GLN E 384 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR E 388 " --> pdb=" O PRO E 385 " (cutoff:3.500A) Proline residue: E 389 - end of helix Processing helix chain 'E' and resid 410 through 418 Processing helix chain 'E' and resid 431 through 443 Processing helix chain 'E' and resid 453 through 458 removed outlier: 3.942A pdb=" N LYS E 458 " --> pdb=" O GLU E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 486 through 491 removed outlier: 3.953A pdb=" N VAL E 490 " --> pdb=" O GLY E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 511 Processing helix chain 'E' and resid 525 through 529 Processing helix chain 'E' and resid 530 through 534 Processing helix chain 'E' and resid 548 through 560 Processing helix chain 'E' and resid 563 through 568 Processing helix chain 'E' and resid 568 through 574 removed outlier: 3.839A pdb=" N GLU E 574 " --> pdb=" O ILE E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 596 Processing helix chain 'G' and resid 40 through 51 removed outlier: 3.516A pdb=" N LYS G 51 " --> pdb=" O PHE G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 59 removed outlier: 3.582A pdb=" N ALA G 55 " --> pdb=" O LYS G 51 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 78 removed outlier: 3.611A pdb=" N GLU G 78 " --> pdb=" O HIS G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 88 removed outlier: 4.028A pdb=" N PHE G 82 " --> pdb=" O GLU G 78 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN G 88 " --> pdb=" O ALA G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 118 Processing helix chain 'G' and resid 161 through 174 removed outlier: 4.255A pdb=" N LYS G 167 " --> pdb=" O GLY G 163 " (cutoff:3.500A) Proline residue: G 170 - end of helix Processing helix chain 'G' and resid 183 through 185 No H-bonds generated for 'chain 'G' and resid 183 through 185' Processing helix chain 'G' and resid 186 through 200 removed outlier: 4.064A pdb=" N THR G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA G 192 " --> pdb=" O GLN G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 222 removed outlier: 3.620A pdb=" N LEU G 222 " --> pdb=" O LEU G 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 242 removed outlier: 3.531A pdb=" N VAL G 242 " --> pdb=" O GLN G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 249 Processing helix chain 'G' and resid 273 through 289 removed outlier: 3.809A pdb=" N ALA G 277 " --> pdb=" O GLN G 273 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 293 Processing helix chain 'G' and resid 307 through 321 removed outlier: 3.923A pdb=" N LYS G 321 " --> pdb=" O ALA G 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 356 Processing helix chain 'G' and resid 384 through 393 removed outlier: 3.648A pdb=" N GLU G 387 " --> pdb=" O GLN G 384 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR G 388 " --> pdb=" O PRO G 385 " (cutoff:3.500A) Proline residue: G 389 - end of helix Processing helix chain 'G' and resid 410 through 418 Processing helix chain 'G' and resid 431 through 443 Processing helix chain 'G' and resid 455 through 459 removed outlier: 3.728A pdb=" N LYS G 458 " --> pdb=" O GLU G 455 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU G 459 " --> pdb=" O SER G 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 455 through 459' Processing helix chain 'G' and resid 475 through 479 Processing helix chain 'G' and resid 486 through 492 removed outlier: 4.021A pdb=" N VAL G 490 " --> pdb=" O GLY G 486 " (cutoff:3.500A) Processing helix chain 'G' and resid 502 through 511 Processing helix chain 'G' and resid 525 through 529 Processing helix chain 'G' and resid 530 through 534 Processing helix chain 'G' and resid 548 through 560 Processing helix chain 'G' and resid 563 through 568 Processing helix chain 'G' and resid 568 through 574 removed outlier: 3.583A pdb=" N GLU G 574 " --> pdb=" O ILE G 570 " (cutoff:3.500A) Processing helix chain 'G' and resid 583 through 596 Processing helix chain 'I' and resid 40 through 51 Processing helix chain 'I' and resid 51 through 59 removed outlier: 3.653A pdb=" N ALA I 55 " --> pdb=" O LYS I 51 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET I 59 " --> pdb=" O ALA I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 78 removed outlier: 3.624A pdb=" N GLU I 78 " --> pdb=" O HIS I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 88 removed outlier: 3.966A pdb=" N PHE I 82 " --> pdb=" O GLU I 78 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN I 88 " --> pdb=" O ALA I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 118 Processing helix chain 'I' and resid 161 through 175 removed outlier: 3.995A pdb=" N LYS I 167 " --> pdb=" O GLY I 163 " (cutoff:3.500A) Proline residue: I 170 - end of helix Processing helix chain 'I' and resid 183 through 185 No H-bonds generated for 'chain 'I' and resid 183 through 185' Processing helix chain 'I' and resid 186 through 200 removed outlier: 4.037A pdb=" N THR I 190 " --> pdb=" O THR I 186 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA I 192 " --> pdb=" O GLN I 188 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET I 193 " --> pdb=" O LEU I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 218 through 222 Processing helix chain 'I' and resid 233 through 242 removed outlier: 3.662A pdb=" N VAL I 242 " --> pdb=" O GLN I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 243 through 249 Processing helix chain 'I' and resid 273 through 289 removed outlier: 3.903A pdb=" N ALA I 277 " --> pdb=" O GLN I 273 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 292 No H-bonds generated for 'chain 'I' and resid 290 through 292' Processing helix chain 'I' and resid 307 through 321 removed outlier: 3.918A pdb=" N LYS I 321 " --> pdb=" O ALA I 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 356 Processing helix chain 'I' and resid 388 through 393 Processing helix chain 'I' and resid 410 through 418 Processing helix chain 'I' and resid 431 through 443 Processing helix chain 'I' and resid 455 through 459 removed outlier: 3.703A pdb=" N LYS I 458 " --> pdb=" O GLU I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 479 Processing helix chain 'I' and resid 486 through 491 removed outlier: 3.924A pdb=" N VAL I 490 " --> pdb=" O GLY I 486 " (cutoff:3.500A) Processing helix chain 'I' and resid 502 through 511 Processing helix chain 'I' and resid 525 through 529 Processing helix chain 'I' and resid 530 through 534 Processing helix chain 'I' and resid 548 through 560 Processing helix chain 'I' and resid 563 through 568 Processing helix chain 'I' and resid 568 through 574 removed outlier: 3.755A pdb=" N GLU I 574 " --> pdb=" O ILE I 570 " (cutoff:3.500A) Processing helix chain 'I' and resid 583 through 596 Processing helix chain 'K' and resid 40 through 58 removed outlier: 4.375A pdb=" N ALA K 53 " --> pdb=" O ILE K 49 " (cutoff:3.500A) Proline residue: K 54 - end of helix Processing helix chain 'K' and resid 60 through 78 removed outlier: 3.628A pdb=" N GLU K 78 " --> pdb=" O HIS K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 88 removed outlier: 4.028A pdb=" N PHE K 82 " --> pdb=" O GLU K 78 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN K 88 " --> pdb=" O ALA K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 118 Processing helix chain 'K' and resid 161 through 174 removed outlier: 4.142A pdb=" N LYS K 167 " --> pdb=" O GLY K 163 " (cutoff:3.500A) Proline residue: K 170 - end of helix Processing helix chain 'K' and resid 183 through 185 No H-bonds generated for 'chain 'K' and resid 183 through 185' Processing helix chain 'K' and resid 186 through 201 removed outlier: 4.104A pdb=" N THR K 190 " --> pdb=" O THR K 186 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY K 201 " --> pdb=" O ILE K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 218 through 222 removed outlier: 3.761A pdb=" N LEU K 222 " --> pdb=" O LEU K 219 " (cutoff:3.500A) Processing helix chain 'K' and resid 233 through 242 removed outlier: 3.675A pdb=" N VAL K 242 " --> pdb=" O GLN K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 249 Processing helix chain 'K' and resid 273 through 289 removed outlier: 3.868A pdb=" N ALA K 277 " --> pdb=" O GLN K 273 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 293 Processing helix chain 'K' and resid 307 through 321 removed outlier: 3.792A pdb=" N LYS K 321 " --> pdb=" O ALA K 317 " (cutoff:3.500A) Processing helix chain 'K' and resid 339 through 356 Processing helix chain 'K' and resid 388 through 393 Processing helix chain 'K' and resid 410 through 418 Processing helix chain 'K' and resid 431 through 443 Processing helix chain 'K' and resid 453 through 458 removed outlier: 3.945A pdb=" N LYS K 458 " --> pdb=" O GLU K 454 " (cutoff:3.500A) Processing helix chain 'K' and resid 475 through 479 Processing helix chain 'K' and resid 486 through 491 removed outlier: 3.955A pdb=" N VAL K 490 " --> pdb=" O GLY K 486 " (cutoff:3.500A) Processing helix chain 'K' and resid 502 through 511 Processing helix chain 'K' and resid 525 through 529 Processing helix chain 'K' and resid 530 through 534 Processing helix chain 'K' and resid 548 through 560 Processing helix chain 'K' and resid 563 through 568 Processing helix chain 'K' and resid 568 through 574 removed outlier: 3.877A pdb=" N GLU K 574 " --> pdb=" O ILE K 570 " (cutoff:3.500A) Processing helix chain 'K' and resid 583 through 596 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 6 through 8 Processing sheet with id=AA3, first strand: chain 'A' and resid 124 through 125 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 124 through 125 current: chain 'A' and resid 139 through 146 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 494 through 501 current: chain 'I' and resid 298 through 304 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 298 through 304 current: chain 'I' and resid 378 through 381 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 400 through 406 current: chain 'I' and resid 446 through 452 Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 210 removed outlier: 6.199A pdb=" N ALA A 151 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LYS A 181 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N HIS A 153 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 261 through 265 removed outlier: 6.609A pdb=" N ASN A 261 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ILE A 301 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N CYS A 263 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N VAL A 303 " --> pdb=" O CYS A 263 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU A 265 " --> pdb=" O VAL A 303 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 298 through 304 current: chain 'A' and resid 378 through 381 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 400 through 406 current: chain 'A' and resid 446 through 452 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 446 through 452 current: chain 'I' and resid 139 through 146 Processing sheet with id=AA6, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AA7, first strand: chain 'A' and resid 539 through 541 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 539 through 541 current: chain 'A' and resid 646 through 656 removed outlier: 6.324A pdb=" N GLY A 647 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU A 671 " --> pdb=" O GLY A 647 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL A 649 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU A 669 " --> pdb=" O VAL A 649 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TRP A 651 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER A 667 " --> pdb=" O TRP A 651 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL A 653 " --> pdb=" O LEU A 665 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU A 665 " --> pdb=" O VAL A 653 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL A 655 " --> pdb=" O VAL A 663 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 662 through 673 current: chain 'I' and resid 646 through 656 removed outlier: 6.320A pdb=" N GLY I 647 " --> pdb=" O LEU I 671 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU I 671 " --> pdb=" O GLY I 647 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL I 649 " --> pdb=" O LEU I 669 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU I 669 " --> pdb=" O VAL I 649 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TRP I 651 " --> pdb=" O SER I 667 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER I 667 " --> pdb=" O TRP I 651 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL I 653 " --> pdb=" O LEU I 665 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU I 665 " --> pdb=" O VAL I 653 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL I 655 " --> pdb=" O VAL I 663 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 6 through 8 Processing sheet with id=AA9, first strand: chain 'B' and resid 20 through 23 Processing sheet with id=AB1, first strand: chain 'B' and resid 124 through 125 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 124 through 125 current: chain 'B' and resid 139 through 146 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 494 through 501 current: chain 'K' and resid 298 through 304 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 298 through 304 current: chain 'K' and resid 378 through 381 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 400 through 406 current: chain 'K' and resid 446 through 452 Processing sheet with id=AB2, first strand: chain 'B' and resid 208 through 210 removed outlier: 6.371A pdb=" N ALA B 178 " --> pdb=" O SER B 209 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 151 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LYS B 181 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N HIS B 153 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 261 through 265 removed outlier: 6.644A pdb=" N ASN B 261 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ILE B 301 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N CYS B 263 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL B 303 " --> pdb=" O CYS B 263 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B 265 " --> pdb=" O VAL B 303 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 298 through 304 current: chain 'B' and resid 378 through 381 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 400 through 406 current: chain 'B' and resid 446 through 452 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 446 through 452 current: chain 'K' and resid 139 through 146 Processing sheet with id=AB4, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AB5, first strand: chain 'B' and resid 539 through 541 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 539 through 541 current: chain 'B' and resid 646 through 656 removed outlier: 6.439A pdb=" N GLY B 647 " --> pdb=" O LEU B 671 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU B 671 " --> pdb=" O GLY B 647 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL B 649 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU B 669 " --> pdb=" O VAL B 649 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TRP B 651 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER B 667 " --> pdb=" O TRP B 651 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL B 653 " --> pdb=" O LEU B 665 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU B 665 " --> pdb=" O VAL B 653 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL B 655 " --> pdb=" O VAL B 663 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 662 through 673 current: chain 'K' and resid 646 through 656 removed outlier: 3.635A pdb=" N ALA K 664 " --> pdb=" O VAL K 655 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 6 through 8 Processing sheet with id=AB7, first strand: chain 'E' and resid 20 through 23 Processing sheet with id=AB8, first strand: chain 'E' and resid 124 through 125 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 124 through 125 current: chain 'E' and resid 139 through 146 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 494 through 501 current: chain 'G' and resid 298 through 304 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 298 through 304 current: chain 'G' and resid 378 through 381 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 400 through 406 current: chain 'G' and resid 446 through 452 Processing sheet with id=AB9, first strand: chain 'E' and resid 208 through 210 removed outlier: 6.365A pdb=" N ALA E 151 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LYS E 181 " --> pdb=" O ALA E 151 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N HIS E 153 " --> pdb=" O LYS E 181 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL E 228 " --> pdb=" O THR E 254 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLU E 256 " --> pdb=" O VAL E 228 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE E 230 " --> pdb=" O GLU E 256 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 261 through 265 removed outlier: 6.583A pdb=" N ASN E 261 " --> pdb=" O ARG E 299 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ILE E 301 " --> pdb=" O ASN E 261 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N CYS E 263 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL E 303 " --> pdb=" O CYS E 263 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU E 265 " --> pdb=" O VAL E 303 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 298 through 304 current: chain 'E' and resid 378 through 381 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 400 through 406 current: chain 'E' and resid 446 through 452 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 446 through 452 current: chain 'G' and resid 139 through 146 Processing sheet with id=AC2, first strand: chain 'E' and resid 472 through 473 Processing sheet with id=AC3, first strand: chain 'E' and resid 539 through 541 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 539 through 541 current: chain 'E' and resid 646 through 656 removed outlier: 3.633A pdb=" N ALA E 664 " --> pdb=" O VAL E 655 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 662 through 673 current: chain 'G' and resid 646 through 656 removed outlier: 6.385A pdb=" N GLY G 647 " --> pdb=" O LEU G 671 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU G 671 " --> pdb=" O GLY G 647 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL G 649 " --> pdb=" O LEU G 669 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU G 669 " --> pdb=" O VAL G 649 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TRP G 651 " --> pdb=" O SER G 667 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER G 667 " --> pdb=" O TRP G 651 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL G 653 " --> pdb=" O LEU G 665 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU G 665 " --> pdb=" O VAL G 653 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL G 655 " --> pdb=" O VAL G 663 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 6 through 8 Processing sheet with id=AC5, first strand: chain 'G' and resid 20 through 23 Processing sheet with id=AC6, first strand: chain 'G' and resid 208 through 210 removed outlier: 6.312A pdb=" N ALA G 178 " --> pdb=" O SER G 209 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ALA G 151 " --> pdb=" O ILE G 179 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LYS G 181 " --> pdb=" O ALA G 151 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N HIS G 153 " --> pdb=" O LYS G 181 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 472 through 473 Processing sheet with id=AC8, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AC9, first strand: chain 'I' and resid 6 through 8 Processing sheet with id=AD1, first strand: chain 'I' and resid 208 through 210 removed outlier: 6.190A pdb=" N ALA I 151 " --> pdb=" O ILE I 179 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LYS I 181 " --> pdb=" O ALA I 151 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N HIS I 153 " --> pdb=" O LYS I 181 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 472 through 473 Processing sheet with id=AD3, first strand: chain 'K' and resid 6 through 8 Processing sheet with id=AD4, first strand: chain 'K' and resid 20 through 23 Processing sheet with id=AD5, first strand: chain 'K' and resid 208 through 210 removed outlier: 6.370A pdb=" N ALA K 151 " --> pdb=" O ILE K 179 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LYS K 181 " --> pdb=" O ALA K 151 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N HIS K 153 " --> pdb=" O LYS K 181 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL K 228 " --> pdb=" O THR K 254 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N GLU K 256 " --> pdb=" O VAL K 228 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHE K 230 " --> pdb=" O GLU K 256 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 472 through 473 1198 hydrogen bonds defined for protein. 3312 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.03 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10325 1.34 - 1.46: 4227 1.46 - 1.57: 16528 1.57 - 1.69: 0 1.69 - 1.81: 240 Bond restraints: 31320 Sorted by residual: bond pdb=" N ARG E 523 " pdb=" CA ARG E 523 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.23e-02 6.61e+03 5.56e+00 bond pdb=" C ASP I 272 " pdb=" N GLN I 273 " ideal model delta sigma weight residual 1.327 1.376 -0.049 2.86e-02 1.22e+03 2.88e+00 bond pdb=" N ARG K 523 " pdb=" CA ARG K 523 " ideal model delta sigma weight residual 1.456 1.475 -0.019 1.23e-02 6.61e+03 2.34e+00 bond pdb=" CG1 ILE A 180 " pdb=" CD1 ILE A 180 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.17e+00 bond pdb=" CG1 ILE G 180 " pdb=" CD1 ILE G 180 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.11e+00 ... (remaining 31315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 41076 1.80 - 3.59: 1211 3.59 - 5.39: 172 5.39 - 7.19: 49 7.19 - 8.99: 8 Bond angle restraints: 42516 Sorted by residual: angle pdb=" C ASP A 522 " pdb=" N ARG A 523 " pdb=" CA ARG A 523 " ideal model delta sigma weight residual 121.54 129.52 -7.98 1.91e+00 2.74e-01 1.75e+01 angle pdb=" N ARG G 523 " pdb=" CA ARG G 523 " pdb=" CB ARG G 523 " ideal model delta sigma weight residual 114.17 109.93 4.24 1.14e+00 7.69e-01 1.38e+01 angle pdb=" N ARG A 523 " pdb=" CA ARG A 523 " pdb=" CB ARG A 523 " ideal model delta sigma weight residual 110.49 116.41 -5.92 1.69e+00 3.50e-01 1.23e+01 angle pdb=" C GLU E 610 " pdb=" N SER E 611 " pdb=" CA SER E 611 " ideal model delta sigma weight residual 122.76 117.23 5.53 1.63e+00 3.76e-01 1.15e+01 angle pdb=" C LEU I 594 " pdb=" N PHE I 595 " pdb=" CA PHE I 595 " ideal model delta sigma weight residual 122.11 116.65 5.46 1.64e+00 3.72e-01 1.11e+01 ... (remaining 42511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 17180 17.92 - 35.85: 1293 35.85 - 53.77: 254 53.77 - 71.70: 76 71.70 - 89.62: 37 Dihedral angle restraints: 18840 sinusoidal: 7296 harmonic: 11544 Sorted by residual: dihedral pdb=" CA LEU I 609 " pdb=" C LEU I 609 " pdb=" N GLU I 610 " pdb=" CA GLU I 610 " ideal model delta harmonic sigma weight residual -180.00 -156.80 -23.20 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA LEU A 609 " pdb=" C LEU A 609 " pdb=" N GLU A 610 " pdb=" CA GLU A 610 " ideal model delta harmonic sigma weight residual -180.00 -156.85 -23.15 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA GLU B 521 " pdb=" C GLU B 521 " pdb=" N ASP B 522 " pdb=" CA ASP B 522 " ideal model delta harmonic sigma weight residual 180.00 -157.12 -22.88 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 18837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3010 0.039 - 0.077: 1268 0.077 - 0.116: 446 0.116 - 0.155: 99 0.155 - 0.193: 19 Chirality restraints: 4842 Sorted by residual: chirality pdb=" CA GLU I 610 " pdb=" N GLU I 610 " pdb=" C GLU I 610 " pdb=" CB GLU I 610 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" CA GLU A 610 " pdb=" N GLU A 610 " pdb=" C GLU A 610 " pdb=" CB GLU A 610 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" CG LEU I 628 " pdb=" CB LEU I 628 " pdb=" CD1 LEU I 628 " pdb=" CD2 LEU I 628 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.89e-01 ... (remaining 4839 not shown) Planarity restraints: 5580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 98 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.98e+00 pdb=" C VAL A 98 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL A 98 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP A 99 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 98 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" C VAL I 98 " 0.038 2.00e-02 2.50e+03 pdb=" O VAL I 98 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP I 99 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 502 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO A 503 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 503 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 503 " -0.030 5.00e-02 4.00e+02 ... (remaining 5577 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 545 2.68 - 3.23: 29509 3.23 - 3.79: 50546 3.79 - 4.34: 70191 4.34 - 4.90: 113152 Nonbonded interactions: 263943 Sorted by model distance: nonbonded pdb=" OE2 GLU I 256 " pdb=" O HOH I 701 " model vdw 2.123 3.040 nonbonded pdb=" OE2 GLU E 256 " pdb=" O HOH E 701 " model vdw 2.166 3.040 nonbonded pdb=" O ILE I 509 " pdb=" NZ LYS I 511 " model vdw 2.186 3.120 nonbonded pdb=" OE2 GLU G 256 " pdb=" O HOH G 701 " model vdw 2.188 3.040 nonbonded pdb=" OG1 THR G 461 " pdb=" O HOH G 702 " model vdw 2.200 3.040 ... (remaining 263938 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 514 or resid 516 through 679)) selection = (chain 'B' and (resid 2 through 514 or resid 516 through 679)) selection = (chain 'E' and (resid 2 through 514 or resid 516 through 679)) selection = (chain 'G' and (resid 2 through 514 or resid 516 through 679)) selection = (chain 'I' and (resid 2 through 514 or resid 516 through 679)) selection = (chain 'K' and (resid 2 through 514 or resid 516 through 679)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 30.590 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 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 0.077 31320 Z= 0.255 Angle : 0.768 8.987 42516 Z= 0.431 Chirality : 0.049 0.193 4842 Planarity : 0.005 0.054 5580 Dihedral : 14.306 89.620 11424 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.03 % Allowed : 1.79 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.12), residues: 4062 helix: -0.80 (0.12), residues: 1428 sheet: -0.20 (0.18), residues: 786 loop : -1.27 (0.12), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 444 TYR 0.021 0.003 TYR B 493 PHE 0.027 0.002 PHE I 595 TRP 0.016 0.002 TRP I 651 HIS 0.006 0.001 HIS B 583 Details of bonding type rmsd covalent geometry : bond 0.00572 (31320) covalent geometry : angle 0.76764 (42516) hydrogen bonds : bond 0.15289 ( 1198) hydrogen bonds : angle 6.09992 ( 3312) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 492 time to evaluate : 0.848 Fit side-chains REVERT: A 339 ASN cc_start: 0.7619 (m-40) cc_final: 0.7347 (m-40) REVERT: A 384 GLN cc_start: 0.7012 (mm-40) cc_final: 0.6688 (mm-40) REVERT: A 394 THR cc_start: 0.8315 (m) cc_final: 0.8091 (m) REVERT: A 410 ARG cc_start: 0.7026 (ttm-80) cc_final: 0.6820 (ttm-80) REVERT: A 414 GLN cc_start: 0.7509 (mt0) cc_final: 0.7293 (mt0) REVERT: A 577 PHE cc_start: 0.7561 (m-80) cc_final: 0.7291 (m-80) REVERT: B 20 ARG cc_start: 0.6442 (mtp85) cc_final: 0.6176 (mmm160) REVERT: B 73 LYS cc_start: 0.8057 (mttm) cc_final: 0.7778 (mttt) REVERT: B 159 PHE cc_start: 0.8338 (m-80) cc_final: 0.8077 (m-80) REVERT: B 318 ARG cc_start: 0.7147 (ttt90) cc_final: 0.6880 (ttm170) REVERT: E 21 LEU cc_start: 0.8341 (mp) cc_final: 0.8041 (mm) REVERT: E 41 MET cc_start: 0.8315 (mmt) cc_final: 0.7533 (mmm) REVERT: E 46 GLN cc_start: 0.7816 (tp-100) cc_final: 0.7607 (tp40) REVERT: E 81 ARG cc_start: 0.7077 (ttm110) cc_final: 0.6647 (mtm110) REVERT: E 414 GLN cc_start: 0.7668 (mt0) cc_final: 0.7435 (mt0) REVERT: G 73 LYS cc_start: 0.8055 (mttm) cc_final: 0.7788 (mttt) REVERT: G 159 PHE cc_start: 0.8341 (m-80) cc_final: 0.8100 (m-80) REVERT: G 199 ASP cc_start: 0.7803 (m-30) cc_final: 0.7498 (m-30) REVERT: I 20 ARG cc_start: 0.6860 (mtp-110) cc_final: 0.6163 (ttm-80) REVERT: I 37 GLU cc_start: 0.6835 (tt0) cc_final: 0.6503 (mt-10) REVERT: I 46 GLN cc_start: 0.7733 (tp40) cc_final: 0.7491 (tp40) REVERT: I 384 GLN cc_start: 0.7016 (mm110) cc_final: 0.6587 (mm-40) REVERT: I 394 THR cc_start: 0.8266 (m) cc_final: 0.8051 (m) REVERT: I 414 GLN cc_start: 0.7462 (mt0) cc_final: 0.7231 (mt0) REVERT: K 8 LEU cc_start: 0.8229 (pp) cc_final: 0.7904 (mp) REVERT: K 41 MET cc_start: 0.8269 (mmt) cc_final: 0.7512 (mmm) REVERT: K 81 ARG cc_start: 0.7074 (ttm110) cc_final: 0.6659 (mtm110) REVERT: K 414 GLN cc_start: 0.7638 (mt0) cc_final: 0.7251 (mt0) outliers start: 0 outliers final: 2 residues processed: 492 average time/residue: 0.7957 time to fit residues: 441.1710 Evaluate side-chains 401 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 399 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain I residue 576 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 0.8980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 8.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 339 ASN A 407 GLN A 409 GLN A 450 GLN A 492 HIS B 13 GLN B 158 ASN B 309 ASN B 492 HIS E 492 HIS ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 158 ASN G 309 ASN I 339 ASN I 409 GLN I 450 GLN K 3 GLN K 46 GLN K 221 HIS K 320 GLN K 492 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.137190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.101076 restraints weight = 60187.796| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.06 r_work: 0.2998 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31320 Z= 0.134 Angle : 0.592 8.295 42516 Z= 0.310 Chirality : 0.044 0.167 4842 Planarity : 0.004 0.049 5580 Dihedral : 5.000 36.004 4354 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.04 % Allowed : 7.48 % Favored : 91.48 % 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 aren not related in a simple way. whole: -0.17 (0.12), residues: 4062 helix: 0.64 (0.13), residues: 1434 sheet: 0.15 (0.18), residues: 780 loop : -0.75 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 410 TYR 0.023 0.002 TYR E 607 PHE 0.026 0.002 PHE E 595 TRP 0.011 0.001 TRP I 651 HIS 0.006 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00296 (31320) covalent geometry : angle 0.59212 (42516) hydrogen bonds : bond 0.04831 ( 1198) hydrogen bonds : angle 4.94848 ( 3312) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 405 time to evaluate : 0.750 Fit side-chains REVERT: A 20 ARG cc_start: 0.7181 (mtp85) cc_final: 0.6702 (mtp-110) REVERT: A 339 ASN cc_start: 0.7278 (m110) cc_final: 0.7032 (m-40) REVERT: A 384 GLN cc_start: 0.7104 (mm-40) cc_final: 0.6801 (mp10) REVERT: A 410 ARG cc_start: 0.7550 (ttm-80) cc_final: 0.7333 (ttm-80) REVERT: A 521 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7764 (mt-10) REVERT: A 577 PHE cc_start: 0.7630 (m-10) cc_final: 0.7378 (m-80) REVERT: B 13 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7865 (pt0) REVERT: B 20 ARG cc_start: 0.6732 (mtp85) cc_final: 0.6295 (mmm160) REVERT: B 73 LYS cc_start: 0.8352 (mttm) cc_final: 0.8083 (mttt) REVERT: B 318 ARG cc_start: 0.7236 (ttt90) cc_final: 0.6903 (ttm170) REVERT: B 359 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7246 (mt-10) REVERT: E 20 ARG cc_start: 0.7066 (mtp85) cc_final: 0.6498 (ttm-80) REVERT: E 21 LEU cc_start: 0.8204 (mp) cc_final: 0.8001 (mm) REVERT: E 33 GLU cc_start: 0.7695 (tt0) cc_final: 0.7321 (tm-30) REVERT: E 41 MET cc_start: 0.8317 (mmt) cc_final: 0.7715 (mmm) REVERT: E 46 GLN cc_start: 0.8176 (tp-100) cc_final: 0.7925 (tp40) REVERT: E 81 ARG cc_start: 0.7165 (ttm110) cc_final: 0.6653 (mtm110) REVERT: E 318 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.5712 (tpt170) REVERT: E 365 GLN cc_start: 0.6918 (tp40) cc_final: 0.6648 (tm-30) REVERT: E 388 THR cc_start: 0.7048 (m) cc_final: 0.6809 (m) REVERT: E 410 ARG cc_start: 0.7822 (ttm170) cc_final: 0.7410 (ttm-80) REVERT: E 414 GLN cc_start: 0.7952 (mt0) cc_final: 0.7694 (mt0) REVERT: G 73 LYS cc_start: 0.8348 (mttm) cc_final: 0.8086 (mttt) REVERT: I 20 ARG cc_start: 0.7220 (mtp-110) cc_final: 0.6944 (mtp-110) REVERT: I 37 GLU cc_start: 0.7049 (tt0) cc_final: 0.6706 (mt-10) REVERT: I 384 GLN cc_start: 0.7138 (mm110) cc_final: 0.6702 (mp10) REVERT: I 521 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7819 (mt-10) REVERT: K 8 LEU cc_start: 0.8056 (pp) cc_final: 0.7738 (mp) REVERT: K 33 GLU cc_start: 0.7698 (tt0) cc_final: 0.7305 (tt0) REVERT: K 41 MET cc_start: 0.8394 (mmt) cc_final: 0.7729 (mmm) REVERT: K 46 GLN cc_start: 0.8156 (tp-100) cc_final: 0.7918 (tp40) REVERT: K 81 ARG cc_start: 0.7178 (ttm110) cc_final: 0.6680 (mtm110) REVERT: K 318 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.5829 (tpt170) REVERT: K 410 ARG cc_start: 0.7799 (ttm170) cc_final: 0.7405 (ttm-80) REVERT: K 414 GLN cc_start: 0.7966 (mt0) cc_final: 0.7527 (tt0) REVERT: K 458 LYS cc_start: 0.8198 (tmtp) cc_final: 0.7790 (ttmt) outliers start: 31 outliers final: 8 residues processed: 427 average time/residue: 0.7621 time to fit residues: 368.3530 Evaluate side-chains 389 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 375 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain G residue 611 SER Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 521 GLU Chi-restraints excluded: chain I residue 576 ILE Chi-restraints excluded: chain I residue 640 SER Chi-restraints excluded: chain K residue 318 ARG Chi-restraints excluded: chain K residue 640 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 1 optimal weight: 20.0000 chunk 141 optimal weight: 9.9990 chunk 257 optimal weight: 8.9990 chunk 295 optimal weight: 7.9990 chunk 164 optimal weight: 3.9990 chunk 265 optimal weight: 5.9990 chunk 216 optimal weight: 10.0000 chunk 271 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 314 optimal weight: 1.9990 chunk 235 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 329 GLN B 309 ASN B 566 HIS E 309 ASN E 339 ASN G 309 ASN G 566 HIS I 409 GLN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 309 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.135168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.099709 restraints weight = 59597.956| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.85 r_work: 0.2953 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 31320 Z= 0.229 Angle : 0.706 8.449 42516 Z= 0.369 Chirality : 0.049 0.191 4842 Planarity : 0.005 0.052 5580 Dihedral : 5.348 39.211 4354 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.95 % Allowed : 8.71 % Favored : 89.34 % 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 aren not related in a simple way. whole: -0.09 (0.12), residues: 4062 helix: 0.60 (0.13), residues: 1464 sheet: 0.31 (0.19), residues: 786 loop : -0.70 (0.13), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 410 TYR 0.022 0.003 TYR E 607 PHE 0.025 0.002 PHE A 595 TRP 0.015 0.002 TRP I 651 HIS 0.005 0.001 HIS G 583 Details of bonding type rmsd covalent geometry : bond 0.00534 (31320) covalent geometry : angle 0.70552 (42516) hydrogen bonds : bond 0.06090 ( 1198) hydrogen bonds : angle 5.14689 ( 3312) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 386 time to evaluate : 1.028 Fit side-chains REVERT: A 205 GLU cc_start: 0.7750 (tp30) cc_final: 0.7512 (tt0) REVERT: A 339 ASN cc_start: 0.7453 (m110) cc_final: 0.7175 (m-40) REVERT: A 384 GLN cc_start: 0.7173 (mm-40) cc_final: 0.6854 (mp10) REVERT: A 410 ARG cc_start: 0.7649 (ttm-80) cc_final: 0.7446 (ttm-80) REVERT: A 523 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.7176 (ptm-80) REVERT: B 20 ARG cc_start: 0.6799 (mtp85) cc_final: 0.6588 (mmm160) REVERT: B 73 LYS cc_start: 0.8431 (mttm) cc_final: 0.8168 (mttt) REVERT: B 186 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8339 (t) REVERT: B 256 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7958 (tm-30) REVERT: B 318 ARG cc_start: 0.7176 (ttt90) cc_final: 0.6938 (ttm170) REVERT: B 359 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7204 (mt-10) REVERT: B 521 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8108 (mt-10) REVERT: E 8 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7818 (mp) REVERT: E 20 ARG cc_start: 0.7152 (mtp85) cc_final: 0.6579 (ttm-80) REVERT: E 41 MET cc_start: 0.8345 (mmt) cc_final: 0.7779 (mmm) REVERT: E 46 GLN cc_start: 0.8197 (tp-100) cc_final: 0.7989 (tp40) REVERT: E 81 ARG cc_start: 0.7209 (ttm110) cc_final: 0.6715 (mtm110) REVERT: E 195 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7826 (ttpt) REVERT: E 318 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6161 (tpp-160) REVERT: E 365 GLN cc_start: 0.6927 (tp40) cc_final: 0.6671 (tm-30) REVERT: E 410 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7514 (ttm170) REVERT: E 414 GLN cc_start: 0.8062 (mt0) cc_final: 0.7823 (mt0) REVERT: E 610 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7501 (mm-30) REVERT: E 642 GLU cc_start: 0.5729 (pp20) cc_final: 0.5235 (tm-30) REVERT: G 33 GLU cc_start: 0.7576 (tt0) cc_final: 0.7271 (tt0) REVERT: G 73 LYS cc_start: 0.8418 (mttm) cc_final: 0.8156 (mttt) REVERT: G 199 ASP cc_start: 0.8258 (m-30) cc_final: 0.8029 (m-30) REVERT: G 348 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7560 (tm-30) REVERT: G 521 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8194 (mt-10) REVERT: I 20 ARG cc_start: 0.7355 (mtp-110) cc_final: 0.7102 (mtp-110) REVERT: I 37 GLU cc_start: 0.7195 (tt0) cc_final: 0.6851 (mt-10) REVERT: I 205 GLU cc_start: 0.7821 (tp30) cc_final: 0.7578 (tt0) REVERT: I 348 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7452 (tm-30) REVERT: I 359 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7693 (mt-10) REVERT: I 384 GLN cc_start: 0.7208 (mm110) cc_final: 0.6980 (mm-40) REVERT: K 33 GLU cc_start: 0.7884 (tt0) cc_final: 0.7475 (tt0) REVERT: K 41 MET cc_start: 0.8366 (mmt) cc_final: 0.7761 (mmm) REVERT: K 46 GLN cc_start: 0.8126 (tp-100) cc_final: 0.7883 (tp40) REVERT: K 81 ARG cc_start: 0.7235 (ttm110) cc_final: 0.6738 (mtm110) REVERT: K 318 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6173 (tpp-160) REVERT: K 414 GLN cc_start: 0.8057 (mt0) cc_final: 0.7844 (mt0) REVERT: K 610 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7534 (mm-30) REVERT: K 640 SER cc_start: 0.7490 (OUTLIER) cc_final: 0.7157 (p) outliers start: 59 outliers final: 21 residues processed: 420 average time/residue: 0.7856 time to fit residues: 373.3082 Evaluate side-chains 412 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 374 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 523 ARG Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 521 GLU Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 195 LYS Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 410 ARG Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain E residue 610 GLU Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 521 GLU Chi-restraints excluded: chain G residue 611 SER Chi-restraints excluded: chain G residue 640 SER Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 348 GLU Chi-restraints excluded: chain I residue 359 GLU Chi-restraints excluded: chain I residue 576 ILE Chi-restraints excluded: chain I residue 640 SER Chi-restraints excluded: chain I residue 670 THR Chi-restraints excluded: chain K residue 318 ARG Chi-restraints excluded: chain K residue 574 GLU Chi-restraints excluded: chain K residue 610 GLU Chi-restraints excluded: chain K residue 640 SER Chi-restraints excluded: chain K residue 670 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 375 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 147 optimal weight: 9.9990 chunk 280 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 291 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 chunk 324 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 329 GLN B 13 GLN B 309 ASN E 309 ASN G 309 ASN I 409 GLN K 3 GLN K 309 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.135190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.099768 restraints weight = 42857.025| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.52 r_work: 0.2971 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 31320 Z= 0.227 Angle : 0.698 8.974 42516 Z= 0.366 Chirality : 0.049 0.198 4842 Planarity : 0.005 0.061 5580 Dihedral : 5.354 40.164 4354 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.36 % Allowed : 9.18 % Favored : 88.46 % 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 aren not related in a simple way. whole: 0.08 (0.13), residues: 4062 helix: 0.79 (0.13), residues: 1428 sheet: 0.35 (0.19), residues: 786 loop : -0.59 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 410 TYR 0.022 0.003 TYR K 607 PHE 0.026 0.002 PHE E 595 TRP 0.016 0.002 TRP I 651 HIS 0.005 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00529 (31320) covalent geometry : angle 0.69835 (42516) hydrogen bonds : bond 0.05961 ( 1198) hydrogen bonds : angle 5.11547 ( 3312) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 376 time to evaluate : 0.962 Fit side-chains REVERT: A 339 ASN cc_start: 0.7444 (m110) cc_final: 0.7199 (m-40) REVERT: A 348 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7400 (tm-30) REVERT: A 384 GLN cc_start: 0.7178 (mm-40) cc_final: 0.6965 (tp40) REVERT: A 410 ARG cc_start: 0.7640 (ttm-80) cc_final: 0.7435 (ttm-80) REVERT: A 523 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.7159 (ptm-80) REVERT: B 73 LYS cc_start: 0.8402 (mttm) cc_final: 0.8135 (mttt) REVERT: B 186 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8373 (t) REVERT: B 256 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7958 (tm-30) REVERT: B 359 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7231 (mt-10) REVERT: B 521 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8209 (mt-10) REVERT: E 8 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7855 (mp) REVERT: E 20 ARG cc_start: 0.7144 (mtp85) cc_final: 0.6577 (ttm-80) REVERT: E 41 MET cc_start: 0.8351 (mmt) cc_final: 0.7776 (mmm) REVERT: E 46 GLN cc_start: 0.8211 (tp-100) cc_final: 0.7953 (tp40) REVERT: E 81 ARG cc_start: 0.7175 (ttm110) cc_final: 0.6681 (mtm110) REVERT: E 186 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8328 (t) REVERT: E 195 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7806 (ttpt) REVERT: E 318 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.5961 (tpt170) REVERT: E 365 GLN cc_start: 0.6898 (tp40) cc_final: 0.6626 (tm-30) REVERT: E 414 GLN cc_start: 0.8023 (mt0) cc_final: 0.7766 (mt0) REVERT: G 33 GLU cc_start: 0.7460 (tt0) cc_final: 0.7165 (tt0) REVERT: G 73 LYS cc_start: 0.8391 (mttm) cc_final: 0.8125 (mttt) REVERT: G 199 ASP cc_start: 0.8224 (m-30) cc_final: 0.7984 (m-30) REVERT: G 348 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7523 (tm-30) REVERT: G 365 GLN cc_start: 0.7115 (OUTLIER) cc_final: 0.6851 (mm-40) REVERT: G 521 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7975 (mt-10) REVERT: I 20 ARG cc_start: 0.7398 (mtp-110) cc_final: 0.7157 (mtp-110) REVERT: I 37 GLU cc_start: 0.7179 (tt0) cc_final: 0.6863 (mt-10) REVERT: I 348 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7416 (tm-30) REVERT: I 359 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7681 (mt-10) REVERT: I 384 GLN cc_start: 0.7354 (mm110) cc_final: 0.6861 (mm-40) REVERT: K 33 GLU cc_start: 0.7837 (tt0) cc_final: 0.7452 (tt0) REVERT: K 41 MET cc_start: 0.8356 (mmt) cc_final: 0.7750 (mmm) REVERT: K 46 GLN cc_start: 0.8110 (tp-100) cc_final: 0.7903 (tp40) REVERT: K 81 ARG cc_start: 0.7208 (ttm110) cc_final: 0.6711 (mtm110) REVERT: K 186 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8337 (t) REVERT: K 318 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6124 (tpp-160) REVERT: K 414 GLN cc_start: 0.8004 (mt0) cc_final: 0.7798 (mt0) REVERT: K 610 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7429 (mm-30) REVERT: K 640 SER cc_start: 0.7565 (OUTLIER) cc_final: 0.7227 (p) outliers start: 72 outliers final: 33 residues processed: 419 average time/residue: 0.7905 time to fit residues: 374.9256 Evaluate side-chains 422 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 370 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 523 ARG Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 521 GLU Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 195 LYS Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 365 GLN Chi-restraints excluded: chain G residue 521 GLU Chi-restraints excluded: chain G residue 610 GLU Chi-restraints excluded: chain G residue 611 SER Chi-restraints excluded: chain G residue 640 SER Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 348 GLU Chi-restraints excluded: chain I residue 359 GLU Chi-restraints excluded: chain I residue 576 ILE Chi-restraints excluded: chain I residue 640 SER Chi-restraints excluded: chain I residue 670 THR Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 196 SER Chi-restraints excluded: chain K residue 318 ARG Chi-restraints excluded: chain K residue 352 ILE Chi-restraints excluded: chain K residue 574 GLU Chi-restraints excluded: chain K residue 610 GLU Chi-restraints excluded: chain K residue 640 SER Chi-restraints excluded: chain K residue 670 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 174 optimal weight: 10.0000 chunk 390 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 279 optimal weight: 0.0670 chunk 254 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 380 optimal weight: 0.8980 chunk 283 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 278 optimal weight: 1.9990 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 293 GLN B 309 ASN E 309 ASN G 13 GLN G 309 ASN I 409 GLN K 3 GLN K 309 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.138269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.103800 restraints weight = 60611.797| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.09 r_work: 0.3015 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 31320 Z= 0.106 Angle : 0.542 8.734 42516 Z= 0.281 Chirality : 0.042 0.155 4842 Planarity : 0.004 0.047 5580 Dihedral : 4.674 37.584 4354 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.79 % Allowed : 10.09 % Favored : 88.11 % 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 aren not related in a simple way. whole: 0.59 (0.13), residues: 4062 helix: 1.36 (0.13), residues: 1428 sheet: 0.53 (0.19), residues: 786 loop : -0.38 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 410 TYR 0.020 0.002 TYR E 607 PHE 0.026 0.001 PHE E 595 TRP 0.010 0.001 TRP K 651 HIS 0.006 0.001 HIS I 463 Details of bonding type rmsd covalent geometry : bond 0.00226 (31320) covalent geometry : angle 0.54240 (42516) hydrogen bonds : bond 0.04021 ( 1198) hydrogen bonds : angle 4.68275 ( 3312) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 404 time to evaluate : 1.019 Fit side-chains REVERT: A 20 ARG cc_start: 0.7240 (mtp85) cc_final: 0.7010 (mmm160) REVERT: A 205 GLU cc_start: 0.7746 (tp30) cc_final: 0.7541 (tt0) REVERT: A 410 ARG cc_start: 0.7613 (ttm-80) cc_final: 0.7409 (ttm-80) REVERT: A 523 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6977 (ptm-80) REVERT: B 3 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6444 (mt0) REVERT: B 73 LYS cc_start: 0.8397 (mttm) cc_final: 0.8139 (mttt) REVERT: B 186 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8236 (t) REVERT: B 256 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8029 (tm-30) REVERT: B 359 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7300 (mt-10) REVERT: B 389 PRO cc_start: 0.8318 (Cg_endo) cc_final: 0.8103 (Cg_exo) REVERT: E 8 LEU cc_start: 0.8126 (pp) cc_final: 0.7759 (mp) REVERT: E 20 ARG cc_start: 0.7086 (mtp85) cc_final: 0.6497 (ttm-80) REVERT: E 33 GLU cc_start: 0.7819 (tt0) cc_final: 0.7375 (tm-30) REVERT: E 41 MET cc_start: 0.8310 (mmt) cc_final: 0.7746 (mmm) REVERT: E 81 ARG cc_start: 0.7156 (ttm110) cc_final: 0.6679 (mtm110) REVERT: E 186 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8290 (t) REVERT: E 195 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8030 (ttpt) REVERT: E 365 GLN cc_start: 0.6916 (tp40) cc_final: 0.6678 (tm-30) REVERT: E 414 GLN cc_start: 0.8045 (mt0) cc_final: 0.7762 (mt0) REVERT: E 523 ARG cc_start: 0.7377 (ptt-90) cc_final: 0.6869 (ptt180) REVERT: G 13 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7875 (pt0) REVERT: G 33 GLU cc_start: 0.7484 (tt0) cc_final: 0.7232 (tt0) REVERT: G 73 LYS cc_start: 0.8360 (mttm) cc_final: 0.8102 (mttt) REVERT: G 348 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7613 (tm-30) REVERT: G 610 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6781 (mt-10) REVERT: I 20 ARG cc_start: 0.7350 (mtp-110) cc_final: 0.6540 (ttm-80) REVERT: I 37 GLU cc_start: 0.7043 (tt0) cc_final: 0.6745 (mt-10) REVERT: I 205 GLU cc_start: 0.7769 (tp30) cc_final: 0.7540 (tt0) REVERT: I 339 ASN cc_start: 0.7256 (m110) cc_final: 0.7051 (m-40) REVERT: I 348 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: I 385 PRO cc_start: 0.7689 (Cg_endo) cc_final: 0.7348 (Cg_exo) REVERT: I 521 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.8043 (mp0) REVERT: K 33 GLU cc_start: 0.7804 (tt0) cc_final: 0.7418 (tm-30) REVERT: K 41 MET cc_start: 0.8363 (mmt) cc_final: 0.7750 (mmm) REVERT: K 46 GLN cc_start: 0.8257 (tp-100) cc_final: 0.7892 (tp40) REVERT: K 81 ARG cc_start: 0.7185 (ttm110) cc_final: 0.6710 (mtm110) REVERT: K 186 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8299 (t) REVERT: K 318 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.5699 (tpt170) REVERT: K 410 ARG cc_start: 0.7838 (ttm170) cc_final: 0.7470 (ttm-80) REVERT: K 414 GLN cc_start: 0.8048 (mt0) cc_final: 0.7818 (mt0) outliers start: 54 outliers final: 12 residues processed: 437 average time/residue: 0.7533 time to fit residues: 374.6145 Evaluate side-chains 397 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 372 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 523 ARG Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 195 LYS Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 611 SER Chi-restraints excluded: chain G residue 640 SER Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 348 GLU Chi-restraints excluded: chain I residue 521 GLU Chi-restraints excluded: chain I residue 576 ILE Chi-restraints excluded: chain I residue 640 SER Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 318 ARG Chi-restraints excluded: chain K residue 540 LEU Chi-restraints excluded: chain K residue 640 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 175 optimal weight: 20.0000 chunk 384 optimal weight: 10.0000 chunk 372 optimal weight: 10.0000 chunk 294 optimal weight: 20.0000 chunk 247 optimal weight: 0.6980 chunk 395 optimal weight: 9.9990 chunk 400 optimal weight: 8.9990 chunk 387 optimal weight: 10.0000 chunk 199 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 overall best weight: 7.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 293 GLN A 329 GLN A 409 GLN B 309 ASN E 309 ASN ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 309 ASN I 191 GLN I 409 GLN K 3 GLN K 13 GLN K 309 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.134529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.099203 restraints weight = 59954.395| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.84 r_work: 0.2944 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 31320 Z= 0.291 Angle : 0.769 10.034 42516 Z= 0.402 Chirality : 0.052 0.195 4842 Planarity : 0.006 0.058 5580 Dihedral : 5.486 40.098 4354 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.52 % Allowed : 10.44 % Favored : 87.04 % 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 aren not related in a simple way. whole: 0.15 (0.13), residues: 4062 helix: 0.80 (0.13), residues: 1428 sheet: 0.41 (0.19), residues: 786 loop : -0.51 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 410 TYR 0.023 0.004 TYR B 493 PHE 0.025 0.003 PHE A 595 TRP 0.017 0.003 TRP I 651 HIS 0.006 0.002 HIS G 446 Details of bonding type rmsd covalent geometry : bond 0.00682 (31320) covalent geometry : angle 0.76866 (42516) hydrogen bonds : bond 0.06597 ( 1198) hydrogen bonds : angle 5.22061 ( 3312) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 378 time to evaluate : 1.080 Fit side-chains REVERT: A 33 GLU cc_start: 0.7715 (pp20) cc_final: 0.7445 (pp20) REVERT: A 256 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8059 (tt0) REVERT: A 410 ARG cc_start: 0.7679 (ttm-80) cc_final: 0.7470 (ttm-80) REVERT: A 523 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7187 (ptm-80) REVERT: B 73 LYS cc_start: 0.8431 (mttm) cc_final: 0.8162 (mttt) REVERT: B 186 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8377 (t) REVERT: B 199 ASP cc_start: 0.8248 (m-30) cc_final: 0.8031 (m-30) REVERT: B 256 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7837 (tm-30) REVERT: B 359 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7254 (mt-10) REVERT: B 521 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7910 (mt-10) REVERT: E 8 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7882 (mp) REVERT: E 20 ARG cc_start: 0.7260 (mtp85) cc_final: 0.6625 (ttm-80) REVERT: E 41 MET cc_start: 0.8363 (mmt) cc_final: 0.7813 (mmm) REVERT: E 46 GLN cc_start: 0.8247 (tp-100) cc_final: 0.8023 (tp40) REVERT: E 81 ARG cc_start: 0.7249 (ttm110) cc_final: 0.6852 (mtm110) REVERT: E 186 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8336 (t) REVERT: E 195 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7931 (ttpt) REVERT: E 318 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.5840 (tpt170) REVERT: E 365 GLN cc_start: 0.6944 (tp40) cc_final: 0.6700 (tm-30) REVERT: E 414 GLN cc_start: 0.8060 (mt0) cc_final: 0.7789 (mt0) REVERT: E 458 LYS cc_start: 0.8208 (tmtp) cc_final: 0.7900 (tttt) REVERT: E 642 GLU cc_start: 0.5745 (pm20) cc_final: 0.5539 (pp20) REVERT: G 73 LYS cc_start: 0.8421 (mttm) cc_final: 0.8154 (mttt) REVERT: G 348 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7527 (tm-30) REVERT: G 365 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6901 (mm-40) REVERT: I 20 ARG cc_start: 0.7505 (mtp-110) cc_final: 0.6593 (ttm-80) REVERT: I 37 GLU cc_start: 0.7230 (tt0) cc_final: 0.6769 (mt-10) REVERT: I 205 GLU cc_start: 0.7816 (tp30) cc_final: 0.7564 (tt0) REVERT: I 329 GLN cc_start: 0.6035 (mm-40) cc_final: 0.5819 (mm110) REVERT: I 348 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7464 (tm-30) REVERT: I 385 PRO cc_start: 0.7816 (Cg_endo) cc_final: 0.7481 (Cg_exo) REVERT: K 46 GLN cc_start: 0.8130 (tp-100) cc_final: 0.7920 (tp40) REVERT: K 81 ARG cc_start: 0.7247 (ttm110) cc_final: 0.6770 (mtm110) REVERT: K 186 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8347 (t) REVERT: K 318 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6216 (tpp-160) REVERT: K 414 GLN cc_start: 0.8087 (mt0) cc_final: 0.7881 (mt0) outliers start: 77 outliers final: 37 residues processed: 428 average time/residue: 0.7680 time to fit residues: 372.3692 Evaluate side-chains 425 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 373 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 523 ARG Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 518 LYS Chi-restraints excluded: chain B residue 521 GLU Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 195 LYS Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 365 GLN Chi-restraints excluded: chain G residue 518 LYS Chi-restraints excluded: chain G residue 610 GLU Chi-restraints excluded: chain G residue 611 SER Chi-restraints excluded: chain G residue 640 SER Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 348 GLU Chi-restraints excluded: chain I residue 576 ILE Chi-restraints excluded: chain I residue 640 SER Chi-restraints excluded: chain I residue 670 THR Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 196 SER Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 318 ARG Chi-restraints excluded: chain K residue 352 ILE Chi-restraints excluded: chain K residue 540 LEU Chi-restraints excluded: chain K residue 574 GLU Chi-restraints excluded: chain K residue 640 SER Chi-restraints excluded: chain K residue 670 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 390 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 264 optimal weight: 6.9990 chunk 192 optimal weight: 5.9990 chunk 376 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 391 optimal weight: 0.9990 chunk 321 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 293 GLN A 409 GLN B 309 ASN E 309 ASN ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 309 ASN I 191 GLN I 409 GLN K 3 GLN K 309 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.136348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.100325 restraints weight = 56677.415| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.74 r_work: 0.2964 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31320 Z= 0.149 Angle : 0.606 9.230 42516 Z= 0.315 Chirality : 0.045 0.173 4842 Planarity : 0.004 0.049 5580 Dihedral : 5.010 38.494 4354 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.73 % Allowed : 11.32 % Favored : 86.95 % 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 aren not related in a simple way. whole: 0.42 (0.13), residues: 4062 helix: 1.12 (0.13), residues: 1434 sheet: 0.50 (0.19), residues: 786 loop : -0.42 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 410 TYR 0.021 0.002 TYR A 607 PHE 0.026 0.002 PHE E 595 TRP 0.012 0.001 TRP I 651 HIS 0.005 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00339 (31320) covalent geometry : angle 0.60635 (42516) hydrogen bonds : bond 0.04808 ( 1198) hydrogen bonds : angle 4.84962 ( 3312) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 385 time to evaluate : 0.929 Fit side-chains REVERT: A 33 GLU cc_start: 0.7673 (pp20) cc_final: 0.7463 (pp20) REVERT: A 348 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7298 (tm-30) REVERT: A 410 ARG cc_start: 0.7663 (ttm-80) cc_final: 0.7453 (ttm-80) REVERT: A 523 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.7038 (ptm-80) REVERT: A 610 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7227 (mt-10) REVERT: B 73 LYS cc_start: 0.8437 (mttm) cc_final: 0.8174 (mttt) REVERT: B 186 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8337 (t) REVERT: B 256 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8092 (tm-30) REVERT: B 359 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7258 (mt-10) REVERT: B 389 PRO cc_start: 0.8360 (Cg_endo) cc_final: 0.8140 (Cg_exo) REVERT: B 410 ARG cc_start: 0.7430 (ttm-80) cc_final: 0.6933 (ttp-110) REVERT: B 521 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8084 (mt-10) REVERT: E 8 LEU cc_start: 0.8197 (pp) cc_final: 0.7822 (mp) REVERT: E 20 ARG cc_start: 0.7106 (mtp85) cc_final: 0.6517 (ttm-80) REVERT: E 41 MET cc_start: 0.8324 (mmt) cc_final: 0.7777 (mmm) REVERT: E 78 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7596 (mt-10) REVERT: E 81 ARG cc_start: 0.7182 (ttm110) cc_final: 0.6650 (mtm110) REVERT: E 134 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7701 (mptm) REVERT: E 195 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7998 (ttpt) REVERT: E 318 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.5797 (tpt170) REVERT: E 365 GLN cc_start: 0.6902 (tp40) cc_final: 0.6666 (tm-30) REVERT: E 414 GLN cc_start: 0.8037 (mt0) cc_final: 0.7721 (tt0) REVERT: E 458 LYS cc_start: 0.8143 (tmtp) cc_final: 0.7917 (tttt) REVERT: E 523 ARG cc_start: 0.7457 (ptt-90) cc_final: 0.6961 (ptt180) REVERT: G 73 LYS cc_start: 0.8415 (mttm) cc_final: 0.8153 (mttt) REVERT: G 348 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7593 (tm-30) REVERT: I 20 ARG cc_start: 0.7420 (mtp-110) cc_final: 0.7049 (mmm160) REVERT: I 37 GLU cc_start: 0.7203 (tt0) cc_final: 0.6740 (mt-10) REVERT: I 205 GLU cc_start: 0.7870 (tp30) cc_final: 0.7580 (tt0) REVERT: I 329 GLN cc_start: 0.6014 (mm-40) cc_final: 0.5754 (mm110) REVERT: I 339 ASN cc_start: 0.7297 (m110) cc_final: 0.7090 (m-40) REVERT: I 348 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7483 (tm-30) REVERT: I 385 PRO cc_start: 0.7794 (Cg_endo) cc_final: 0.7431 (Cg_exo) REVERT: K 41 MET cc_start: 0.8367 (mmt) cc_final: 0.7707 (mmm) REVERT: K 46 GLN cc_start: 0.8231 (tp-100) cc_final: 0.7973 (tp40) REVERT: K 81 ARG cc_start: 0.7175 (ttm110) cc_final: 0.6684 (mtm110) REVERT: K 186 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8338 (t) REVERT: K 318 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.5781 (tpt170) REVERT: K 414 GLN cc_start: 0.8026 (mt0) cc_final: 0.7813 (mt0) outliers start: 51 outliers final: 22 residues processed: 416 average time/residue: 0.7576 time to fit residues: 357.7822 Evaluate side-chains 414 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 379 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 523 ARG Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 518 LYS Chi-restraints excluded: chain B residue 521 GLU Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain E residue 134 LYS Chi-restraints excluded: chain E residue 195 LYS Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 518 LYS Chi-restraints excluded: chain G residue 611 SER Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 348 GLU Chi-restraints excluded: chain I residue 576 ILE Chi-restraints excluded: chain I residue 640 SER Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 318 ARG Chi-restraints excluded: chain K residue 540 LEU Chi-restraints excluded: chain K residue 574 GLU Chi-restraints excluded: chain K residue 640 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 122 optimal weight: 7.9990 chunk 314 optimal weight: 5.9990 chunk 228 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 324 optimal weight: 5.9990 chunk 395 optimal weight: 0.0970 chunk 319 optimal weight: 10.0000 chunk 142 optimal weight: 0.4980 chunk 16 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 overall best weight: 3.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 329 GLN A 409 GLN B 46 GLN B 309 ASN E 309 ASN ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 309 ASN I 191 GLN I 409 GLN K 3 GLN K 309 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.099916 restraints weight = 56102.456| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.72 r_work: 0.2962 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 31320 Z= 0.172 Angle : 0.639 10.287 42516 Z= 0.331 Chirality : 0.046 0.180 4842 Planarity : 0.005 0.051 5580 Dihedral : 5.088 38.491 4354 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.73 % Allowed : 11.42 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.13), residues: 4062 helix: 1.09 (0.13), residues: 1428 sheet: 0.52 (0.19), residues: 786 loop : -0.40 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 81 TYR 0.020 0.003 TYR E 607 PHE 0.026 0.002 PHE E 595 TRP 0.012 0.002 TRP I 651 HIS 0.005 0.001 HIS I 463 Details of bonding type rmsd covalent geometry : bond 0.00395 (31320) covalent geometry : angle 0.63883 (42516) hydrogen bonds : bond 0.05198 ( 1198) hydrogen bonds : angle 4.90947 ( 3312) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 383 time to evaluate : 1.140 Fit side-chains REVERT: A 33 GLU cc_start: 0.7706 (pp20) cc_final: 0.7470 (pp20) REVERT: A 348 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7422 (tm-30) REVERT: A 410 ARG cc_start: 0.7675 (ttm-80) cc_final: 0.7461 (ttm-80) REVERT: A 523 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.7062 (ptm-80) REVERT: B 73 LYS cc_start: 0.8439 (mttm) cc_final: 0.8174 (mttt) REVERT: B 186 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8337 (t) REVERT: B 256 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8066 (tm-30) REVERT: B 359 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7235 (mt-10) REVERT: B 389 PRO cc_start: 0.8341 (Cg_endo) cc_final: 0.8114 (Cg_exo) REVERT: B 521 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8099 (mt-10) REVERT: E 20 ARG cc_start: 0.7115 (mtp85) cc_final: 0.6527 (ttm-80) REVERT: E 81 ARG cc_start: 0.7210 (ttm110) cc_final: 0.6824 (mtm110) REVERT: E 134 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7685 (mptm) REVERT: E 195 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8012 (ttpt) REVERT: E 318 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.5830 (tpt170) REVERT: E 365 GLN cc_start: 0.6833 (tp40) cc_final: 0.6600 (tm-30) REVERT: E 414 GLN cc_start: 0.8037 (mt0) cc_final: 0.7724 (tt0) REVERT: E 458 LYS cc_start: 0.8143 (tmtp) cc_final: 0.7917 (tttt) REVERT: E 523 ARG cc_start: 0.7465 (ptt-90) cc_final: 0.6975 (ptt180) REVERT: G 73 LYS cc_start: 0.8422 (mttm) cc_final: 0.8156 (mttt) REVERT: G 348 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7569 (tm-30) REVERT: G 365 GLN cc_start: 0.7114 (OUTLIER) cc_final: 0.6893 (mm-40) REVERT: I 20 ARG cc_start: 0.7568 (mtp-110) cc_final: 0.7178 (mmm160) REVERT: I 37 GLU cc_start: 0.7220 (tt0) cc_final: 0.6766 (mt-10) REVERT: I 329 GLN cc_start: 0.6059 (mm-40) cc_final: 0.5784 (mm110) REVERT: I 348 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7461 (tm-30) REVERT: I 385 PRO cc_start: 0.7782 (Cg_endo) cc_final: 0.7443 (Cg_exo) REVERT: K 33 GLU cc_start: 0.7848 (tt0) cc_final: 0.7474 (tt0) REVERT: K 41 MET cc_start: 0.8348 (mmt) cc_final: 0.7695 (mmm) REVERT: K 46 GLN cc_start: 0.8226 (tp-100) cc_final: 0.7959 (tp40) REVERT: K 81 ARG cc_start: 0.7215 (ttm110) cc_final: 0.6836 (mtm110) REVERT: K 318 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.5890 (tpt170) REVERT: K 414 GLN cc_start: 0.8020 (mt0) cc_final: 0.7816 (mt0) outliers start: 51 outliers final: 30 residues processed: 413 average time/residue: 0.8211 time to fit residues: 383.3085 Evaluate side-chains 419 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 376 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 523 ARG Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 518 LYS Chi-restraints excluded: chain B residue 521 GLU Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain E residue 134 LYS Chi-restraints excluded: chain E residue 195 LYS Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 256 GLU Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 365 GLN Chi-restraints excluded: chain G residue 518 LYS Chi-restraints excluded: chain G residue 611 SER Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 348 GLU Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 576 ILE Chi-restraints excluded: chain I residue 640 SER Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 318 ARG Chi-restraints excluded: chain K residue 540 LEU Chi-restraints excluded: chain K residue 574 GLU Chi-restraints excluded: chain K residue 640 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 142 optimal weight: 10.0000 chunk 205 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 249 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 191 optimal weight: 9.9990 chunk 237 optimal weight: 20.0000 chunk 273 optimal weight: 6.9990 chunk 203 optimal weight: 0.1980 chunk 308 optimal weight: 20.0000 chunk 387 optimal weight: 10.0000 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 309 ASN A 409 GLN B 46 GLN B 309 ASN E 309 ASN ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 309 ASN I 409 GLN K 3 GLN K 309 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.100326 restraints weight = 59908.970| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.00 r_work: 0.2978 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31320 Z= 0.176 Angle : 0.640 10.356 42516 Z= 0.333 Chirality : 0.046 0.179 4842 Planarity : 0.005 0.051 5580 Dihedral : 5.085 38.256 4354 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.76 % Allowed : 11.45 % Favored : 86.79 % 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 aren not related in a simple way. whole: 0.43 (0.13), residues: 4062 helix: 1.09 (0.13), residues: 1428 sheet: 0.53 (0.19), residues: 786 loop : -0.39 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 81 TYR 0.021 0.003 TYR K 607 PHE 0.026 0.002 PHE E 595 TRP 0.013 0.002 TRP I 651 HIS 0.005 0.001 HIS I 463 Details of bonding type rmsd covalent geometry : bond 0.00404 (31320) covalent geometry : angle 0.64035 (42516) hydrogen bonds : bond 0.05190 ( 1198) hydrogen bonds : angle 4.90598 ( 3312) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 380 time to evaluate : 1.060 Fit side-chains REVERT: A 33 GLU cc_start: 0.7662 (pp20) cc_final: 0.7418 (pp20) REVERT: A 348 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: A 410 ARG cc_start: 0.7617 (ttm-80) cc_final: 0.7397 (ttm-80) REVERT: A 523 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.7013 (ptm-80) REVERT: A 610 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7228 (mt-10) REVERT: B 73 LYS cc_start: 0.8409 (mttm) cc_final: 0.8136 (mttt) REVERT: B 186 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8335 (t) REVERT: B 256 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8050 (tm-30) REVERT: B 359 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7194 (mt-10) REVERT: B 389 PRO cc_start: 0.8361 (Cg_endo) cc_final: 0.8146 (Cg_exo) REVERT: B 521 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8065 (mt-10) REVERT: E 8 LEU cc_start: 0.8194 (pp) cc_final: 0.7791 (mp) REVERT: E 20 ARG cc_start: 0.7105 (mtp85) cc_final: 0.6515 (ttm-80) REVERT: E 41 MET cc_start: 0.8332 (mmt) cc_final: 0.7715 (mmm) REVERT: E 81 ARG cc_start: 0.7165 (ttm110) cc_final: 0.6775 (mtm110) REVERT: E 134 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7659 (mptm) REVERT: E 195 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7957 (ttpt) REVERT: E 318 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.5804 (tpt170) REVERT: E 365 GLN cc_start: 0.6890 (tp40) cc_final: 0.6649 (tm-30) REVERT: E 410 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7401 (ttm170) REVERT: E 414 GLN cc_start: 0.7981 (mt0) cc_final: 0.7667 (tt0) REVERT: E 458 LYS cc_start: 0.8127 (tmtp) cc_final: 0.7902 (tttt) REVERT: E 523 ARG cc_start: 0.7433 (ptt-90) cc_final: 0.6931 (ptt180) REVERT: G 73 LYS cc_start: 0.8391 (mttm) cc_final: 0.8119 (mttt) REVERT: G 348 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7512 (tm-30) REVERT: I 20 ARG cc_start: 0.7400 (mtp-110) cc_final: 0.7015 (mmm160) REVERT: I 37 GLU cc_start: 0.7188 (tt0) cc_final: 0.6733 (mt-10) REVERT: I 205 GLU cc_start: 0.7602 (tp30) cc_final: 0.7398 (tt0) REVERT: I 348 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7408 (tm-30) REVERT: I 385 PRO cc_start: 0.7800 (Cg_endo) cc_final: 0.7420 (Cg_exo) REVERT: K 41 MET cc_start: 0.8333 (mmt) cc_final: 0.7662 (mmm) REVERT: K 46 GLN cc_start: 0.8181 (tp-100) cc_final: 0.7904 (tp40) REVERT: K 81 ARG cc_start: 0.7166 (ttm110) cc_final: 0.6785 (mtm110) REVERT: K 318 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.5836 (tpt170) REVERT: K 414 GLN cc_start: 0.7970 (mt0) cc_final: 0.7758 (mt0) outliers start: 52 outliers final: 30 residues processed: 412 average time/residue: 0.7577 time to fit residues: 353.1036 Evaluate side-chains 420 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 377 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 523 ARG Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 518 LYS Chi-restraints excluded: chain B residue 521 GLU Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 134 LYS Chi-restraints excluded: chain E residue 195 LYS Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 410 ARG Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 518 LYS Chi-restraints excluded: chain G residue 611 SER Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 348 GLU Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 576 ILE Chi-restraints excluded: chain I residue 640 SER Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 318 ARG Chi-restraints excluded: chain K residue 540 LEU Chi-restraints excluded: chain K residue 574 GLU Chi-restraints excluded: chain K residue 640 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 307 optimal weight: 0.5980 chunk 349 optimal weight: 4.9990 chunk 263 optimal weight: 7.9990 chunk 233 optimal weight: 0.0370 chunk 136 optimal weight: 0.4980 chunk 269 optimal weight: 9.9990 chunk 277 optimal weight: 9.9990 chunk 312 optimal weight: 9.9990 chunk 165 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 409 GLN B 46 GLN B 309 ASN E 309 ASN G 13 GLN G 46 GLN G 309 ASN I 191 GLN I 293 GLN I 329 GLN I 409 GLN K 3 GLN K 13 GLN K 309 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.137787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.102218 restraints weight = 63653.467| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.20 r_work: 0.3005 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31320 Z= 0.117 Angle : 0.563 10.504 42516 Z= 0.290 Chirality : 0.043 0.166 4842 Planarity : 0.004 0.048 5580 Dihedral : 4.707 36.353 4354 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.51 % Allowed : 11.89 % Favored : 86.60 % 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 aren not related in a simple way. whole: 0.71 (0.13), residues: 4062 helix: 1.39 (0.14), residues: 1428 sheet: 0.61 (0.19), residues: 786 loop : -0.25 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 81 TYR 0.020 0.002 TYR E 607 PHE 0.026 0.002 PHE E 595 TRP 0.011 0.001 TRP A 651 HIS 0.005 0.001 HIS I 463 Details of bonding type rmsd covalent geometry : bond 0.00258 (31320) covalent geometry : angle 0.56253 (42516) hydrogen bonds : bond 0.04132 ( 1198) hydrogen bonds : angle 4.66910 ( 3312) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 387 time to evaluate : 1.164 Fit side-chains REVERT: A 33 GLU cc_start: 0.7675 (pp20) cc_final: 0.7408 (pp20) REVERT: A 34 VAL cc_start: 0.8091 (t) cc_final: 0.7667 (p) REVERT: A 81 ARG cc_start: 0.7235 (mtm110) cc_final: 0.6878 (ptp-170) REVERT: A 348 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7181 (tm-30) REVERT: A 410 ARG cc_start: 0.7574 (ttm-80) cc_final: 0.7354 (ttm-80) REVERT: A 523 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6929 (ptm-80) REVERT: A 610 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6973 (mt-10) REVERT: B 73 LYS cc_start: 0.8372 (mttm) cc_final: 0.8105 (mttt) REVERT: B 186 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8293 (t) REVERT: B 256 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8061 (tm-30) REVERT: B 359 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7253 (mt-10) REVERT: B 389 PRO cc_start: 0.8307 (Cg_endo) cc_final: 0.8092 (Cg_exo) REVERT: E 8 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7712 (mp) REVERT: E 20 ARG cc_start: 0.7138 (mtp85) cc_final: 0.6551 (ttm-80) REVERT: E 33 GLU cc_start: 0.7825 (tt0) cc_final: 0.7346 (tm-30) REVERT: E 41 MET cc_start: 0.8287 (mmt) cc_final: 0.7646 (mmm) REVERT: E 81 ARG cc_start: 0.7186 (ttm110) cc_final: 0.6815 (mtm110) REVERT: E 134 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7649 (mptm) REVERT: E 195 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7971 (ttpt) REVERT: E 318 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.5692 (tpt170) REVERT: E 365 GLN cc_start: 0.6815 (tp40) cc_final: 0.6576 (tm-30) REVERT: E 414 GLN cc_start: 0.7970 (mt0) cc_final: 0.7646 (tt0) REVERT: E 458 LYS cc_start: 0.8131 (tmtp) cc_final: 0.7911 (tttt) REVERT: G 73 LYS cc_start: 0.8325 (mttm) cc_final: 0.8054 (mttt) REVERT: G 348 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: G 365 GLN cc_start: 0.7019 (OUTLIER) cc_final: 0.6812 (mm-40) REVERT: G 410 ARG cc_start: 0.7439 (ttm-80) cc_final: 0.6902 (tmt170) REVERT: G 610 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6975 (mt-10) REVERT: I 20 ARG cc_start: 0.7413 (mtp-110) cc_final: 0.7050 (mmm160) REVERT: I 37 GLU cc_start: 0.7116 (tt0) cc_final: 0.6786 (mt-10) REVERT: I 81 ARG cc_start: 0.7242 (mtm110) cc_final: 0.6865 (ptp-170) REVERT: I 205 GLU cc_start: 0.7650 (tp30) cc_final: 0.7439 (tt0) REVERT: I 348 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7250 (tm-30) REVERT: I 385 PRO cc_start: 0.7741 (Cg_endo) cc_final: 0.7448 (Cg_exo) REVERT: I 610 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6962 (mt-10) REVERT: K 33 GLU cc_start: 0.7804 (tt0) cc_final: 0.7395 (tt0) REVERT: K 78 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7410 (mt-10) REVERT: K 81 ARG cc_start: 0.7159 (ttm110) cc_final: 0.6790 (mtm110) REVERT: K 318 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.5683 (tpt170) REVERT: K 414 GLN cc_start: 0.7948 (mt0) cc_final: 0.7735 (mt0) REVERT: K 523 ARG cc_start: 0.7448 (mtm180) cc_final: 0.6994 (ptt-90) outliers start: 44 outliers final: 19 residues processed: 415 average time/residue: 0.7525 time to fit residues: 354.1341 Evaluate side-chains 399 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 367 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 523 ARG Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 518 LYS Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 134 LYS Chi-restraints excluded: chain E residue 195 LYS Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 256 GLU Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 365 GLN Chi-restraints excluded: chain G residue 518 LYS Chi-restraints excluded: chain I residue 348 GLU Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 576 ILE Chi-restraints excluded: chain I residue 640 SER Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 318 ARG Chi-restraints excluded: chain K residue 640 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 219 optimal weight: 7.9990 chunk 154 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 241 optimal weight: 5.9990 chunk 321 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 223 optimal weight: 10.0000 chunk 398 optimal weight: 10.0000 chunk 234 optimal weight: 20.0000 chunk 235 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 293 GLN A 409 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN B 309 ASN E 309 ASN G 13 GLN G 46 GLN G 309 ASN I 191 GLN I 409 GLN K 3 GLN K 309 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.101785 restraints weight = 59533.073| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.84 r_work: 0.2989 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31320 Z= 0.137 Angle : 0.595 10.512 42516 Z= 0.306 Chirality : 0.044 0.172 4842 Planarity : 0.004 0.048 5580 Dihedral : 4.816 36.441 4354 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.38 % Allowed : 12.33 % Favored : 86.29 % 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 aren not related in a simple way. whole: 0.70 (0.13), residues: 4062 helix: 1.32 (0.13), residues: 1434 sheet: 0.61 (0.19), residues: 816 loop : -0.21 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 81 TYR 0.020 0.002 TYR A 607 PHE 0.024 0.002 PHE E 595 TRP 0.011 0.001 TRP G 651 HIS 0.005 0.001 HIS I 463 Details of bonding type rmsd covalent geometry : bond 0.00308 (31320) covalent geometry : angle 0.59458 (42516) hydrogen bonds : bond 0.04584 ( 1198) hydrogen bonds : angle 4.74302 ( 3312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14710.37 seconds wall clock time: 249 minutes 42.36 seconds (14982.36 seconds total)