Starting phenix.real_space_refine on Thu Jun 26 13:52:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wv6_37866/06_2025/8wv6_37866.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wv6_37866/06_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_37866/06_2025/8wv6_37866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wv6_37866/06_2025/8wv6_37866.map" model { file = "/net/cci-nas-00/data/ceres_data/8wv6_37866/06_2025/8wv6_37866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wv6_37866/06_2025/8wv6_37866.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 44.17, per 1000 atoms: 1.43 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: 9.27 Conformation dependent library (CDL) restraints added in 9.4 seconds 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: 5.71 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: 19.53 Time building geometry restraints manager: 10.79 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: 0.07 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: 119.630 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: 0.040 Extract box with map and model: 1.180 Check model and map are aligned: 0.250 Set scattering table: 0.300 Process input model: 120.300 Find NCS groups from input model: 3.190 Set up NCS constraints: 0.320 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: 0.030 Load rotamer database and sin/cos tables:120.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 365.330 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.002 TRP I 651 HIS 0.006 0.001 HIS B 583 PHE 0.027 0.002 PHE I 595 TYR 0.021 0.003 TYR B 493 ARG 0.007 0.001 ARG B 444 Details of bonding type rmsd hydrogen bonds : bond 0.15289 ( 1198) hydrogen bonds : angle 6.09992 ( 3312) covalent geometry : bond 0.00572 (31320) covalent geometry : angle 0.76764 (42516) *********************** 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 : 5.776 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: 0.7499 (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: 2.5448 time to fit residues: 1421.3572 Evaluate side-chains 400 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 398 time to evaluate : 3.369 ------------------------------------------------------------------------------- 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 339 optimal weight: 4.9990 chunk 304 optimal weight: 0.3980 chunk 169 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 205 optimal weight: 8.9990 chunk 162 optimal weight: 8.9990 chunk 315 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 191 optimal weight: 8.9990 chunk 234 optimal weight: 9.9990 chunk 365 optimal weight: 10.0000 overall best weight: 4.4788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN B 158 ASN B 309 ASN B 492 HIS E 191 GLN E 492 HIS ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 GLN G 158 ASN G 309 ASN G 566 HIS I 339 ASN I 409 GLN I 450 GLN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 46 GLN K 221 HIS K 320 GLN K 492 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.135506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.101490 restraints weight = 59002.408| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.98 r_work: 0.2951 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 31320 Z= 0.207 Angle : 0.689 8.675 42516 Z= 0.361 Chirality : 0.048 0.187 4842 Planarity : 0.005 0.054 5580 Dihedral : 5.376 38.479 4354 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.19 % Allowed : 7.64 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.12), residues: 4062 helix: 0.39 (0.13), residues: 1428 sheet: 0.15 (0.18), residues: 786 loop : -0.78 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 651 HIS 0.005 0.001 HIS A 463 PHE 0.026 0.002 PHE E 595 TYR 0.026 0.003 TYR E 607 ARG 0.008 0.001 ARG I 410 Details of bonding type rmsd hydrogen bonds : bond 0.05847 ( 1198) hydrogen bonds : angle 5.15912 ( 3312) covalent geometry : bond 0.00480 (31320) covalent geometry : angle 0.68922 (42516) *********************** 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 427 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 391 time to evaluate : 3.722 Fit side-chains REVERT: A 8 LEU cc_start: 0.8117 (pp) cc_final: 0.7906 (mt) REVERT: A 339 ASN cc_start: 0.7421 (m110) cc_final: 0.7155 (m-40) REVERT: A 384 GLN cc_start: 0.7146 (mm-40) cc_final: 0.6834 (mp10) REVERT: A 410 ARG cc_start: 0.7642 (ttm-80) cc_final: 0.7424 (ttm-80) REVERT: A 521 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7839 (mt-10) REVERT: B 73 LYS cc_start: 0.8423 (mttm) cc_final: 0.8162 (mttt) REVERT: B 159 PHE cc_start: 0.8484 (m-80) cc_final: 0.8254 (m-80) REVERT: B 256 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7990 (tm-30) REVERT: B 318 ARG cc_start: 0.7285 (ttt90) cc_final: 0.6966 (ttm170) REVERT: B 359 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6925 (mt-10) REVERT: E 20 ARG cc_start: 0.7112 (mtp85) cc_final: 0.6531 (ttm-80) REVERT: E 21 LEU cc_start: 0.8263 (mp) cc_final: 0.8030 (mm) REVERT: E 41 MET cc_start: 0.8349 (mmt) cc_final: 0.7776 (mmm) REVERT: E 46 GLN cc_start: 0.8271 (tp-100) cc_final: 0.8021 (tp40) REVERT: E 81 ARG cc_start: 0.7271 (ttm110) cc_final: 0.6742 (mtm110) REVERT: E 318 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6135 (tpp-160) REVERT: E 365 GLN cc_start: 0.6923 (tp40) cc_final: 0.6631 (tm-30) REVERT: E 414 GLN cc_start: 0.8059 (mt0) cc_final: 0.7819 (mt0) REVERT: G 73 LYS cc_start: 0.8425 (mttm) cc_final: 0.8161 (mttt) REVERT: G 159 PHE cc_start: 0.8505 (m-80) cc_final: 0.8270 (m-80) REVERT: G 199 ASP cc_start: 0.8280 (m-30) cc_final: 0.8048 (m-30) REVERT: I 20 ARG cc_start: 0.7336 (mtp-110) cc_final: 0.7096 (mtp-110) REVERT: I 37 GLU cc_start: 0.7124 (tt0) cc_final: 0.6630 (mt-10) REVERT: I 384 GLN cc_start: 0.7227 (mm110) cc_final: 0.6699 (mm-40) REVERT: I 521 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7873 (mt-10) REVERT: K 8 LEU cc_start: 0.8174 (pp) cc_final: 0.7826 (mp) REVERT: K 33 GLU cc_start: 0.7877 (tt0) cc_final: 0.7478 (tt0) REVERT: K 41 MET cc_start: 0.8385 (mmt) cc_final: 0.7769 (mmm) REVERT: K 46 GLN cc_start: 0.8212 (tp-100) cc_final: 0.7989 (tp40) REVERT: K 73 LYS cc_start: 0.8279 (mttt) cc_final: 0.8010 (mttp) REVERT: K 81 ARG cc_start: 0.7283 (ttm110) cc_final: 0.6779 (mtm110) REVERT: K 318 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6241 (tpp-160) REVERT: K 414 GLN cc_start: 0.8068 (mt0) cc_final: 0.7854 (mt0) REVERT: K 458 LYS cc_start: 0.8264 (tmtp) cc_final: 0.7983 (tttt) outliers start: 36 outliers final: 14 residues processed: 418 average time/residue: 1.9343 time to fit residues: 917.0713 Evaluate side-chains 400 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 380 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN 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 256 GLU Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain G residue 321 LYS 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 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 640 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 134 optimal weight: 20.0000 chunk 284 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 337 optimal weight: 8.9990 chunk 390 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 218 optimal weight: 0.9980 chunk 278 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 B 566 HIS E 309 ASN G 309 ASN I 409 GLN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.135477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.099353 restraints weight = 47009.320| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.62 r_work: 0.2963 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 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 = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 31320 Z= 0.209 Angle : 0.685 8.550 42516 Z= 0.358 Chirality : 0.048 0.187 4842 Planarity : 0.005 0.058 5580 Dihedral : 5.336 39.850 4354 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.79 % Allowed : 8.93 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.13), residues: 4062 helix: 0.59 (0.13), residues: 1464 sheet: 0.30 (0.19), residues: 786 loop : -0.68 (0.13), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 651 HIS 0.005 0.001 HIS B 583 PHE 0.027 0.002 PHE E 595 TYR 0.023 0.003 TYR E 607 ARG 0.007 0.001 ARG I 410 Details of bonding type rmsd hydrogen bonds : bond 0.05846 ( 1198) hydrogen bonds : angle 5.11034 ( 3312) covalent geometry : bond 0.00485 (31320) covalent geometry : angle 0.68523 (42516) *********************** 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 440 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 386 time to evaluate : 3.468 Fit side-chains REVERT: A 205 GLU cc_start: 0.7838 (tp30) cc_final: 0.7585 (tt0) REVERT: A 339 ASN cc_start: 0.7423 (m110) cc_final: 0.7196 (m-40) REVERT: A 384 GLN cc_start: 0.7176 (mm-40) cc_final: 0.6855 (mp10) REVERT: A 410 ARG cc_start: 0.7633 (ttm-80) cc_final: 0.7408 (ttm-80) REVERT: B 73 LYS cc_start: 0.8410 (mttm) cc_final: 0.8148 (mttt) REVERT: B 159 PHE cc_start: 0.8514 (m-80) cc_final: 0.8274 (m-80) REVERT: B 186 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8361 (t) REVERT: B 256 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7992 (tm-30) REVERT: B 318 ARG cc_start: 0.7250 (ttt90) cc_final: 0.6957 (ttm170) REVERT: B 359 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7231 (mt-10) REVERT: B 410 ARG cc_start: 0.7489 (ttm-80) cc_final: 0.7085 (ttp-110) REVERT: E 8 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7797 (mp) REVERT: E 20 ARG cc_start: 0.7146 (mtp85) cc_final: 0.6574 (ttm-80) REVERT: E 21 LEU cc_start: 0.8232 (mp) cc_final: 0.8024 (mm) REVERT: E 41 MET cc_start: 0.8352 (mmt) cc_final: 0.7770 (mmm) REVERT: E 46 GLN cc_start: 0.8197 (tp-100) cc_final: 0.7958 (tp40) REVERT: E 81 ARG cc_start: 0.7229 (ttm110) cc_final: 0.6732 (mtm110) REVERT: E 186 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8316 (t) REVERT: E 195 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7805 (ttpt) REVERT: E 318 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.5933 (tpt170) REVERT: E 365 GLN cc_start: 0.6890 (tp40) cc_final: 0.6621 (tm-30) REVERT: E 410 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7503 (ttm170) REVERT: E 414 GLN cc_start: 0.8065 (mt0) cc_final: 0.7823 (mt0) REVERT: E 458 LYS cc_start: 0.8195 (tmtp) cc_final: 0.7735 (ttmt) REVERT: G 73 LYS cc_start: 0.8403 (mttm) cc_final: 0.8143 (mttt) REVERT: G 159 PHE cc_start: 0.8543 (m-80) cc_final: 0.8293 (m-80) REVERT: G 186 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8324 (t) REVERT: G 199 ASP cc_start: 0.8258 (m-30) cc_final: 0.8018 (m-30) REVERT: I 20 ARG cc_start: 0.7277 (mtp-110) cc_final: 0.6984 (mtp-110) REVERT: I 37 GLU cc_start: 0.7219 (tt0) cc_final: 0.6759 (mt-10) REVERT: I 205 GLU cc_start: 0.7819 (tp30) cc_final: 0.7572 (tt0) REVERT: I 359 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7691 (mt-10) REVERT: I 384 GLN cc_start: 0.7344 (mm110) cc_final: 0.6864 (mm-40) REVERT: K 33 GLU cc_start: 0.7862 (tt0) cc_final: 0.7477 (tt0) REVERT: K 41 MET cc_start: 0.8362 (mmt) cc_final: 0.7754 (mmm) REVERT: K 46 GLN cc_start: 0.8124 (tp-100) cc_final: 0.7866 (tp40) REVERT: K 81 ARG cc_start: 0.7245 (ttm110) cc_final: 0.6758 (mtm110) REVERT: K 186 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8320 (t) REVERT: K 318 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.5919 (tpt170) REVERT: K 458 LYS cc_start: 0.8216 (tmtp) cc_final: 0.7926 (tttt) REVERT: K 640 SER cc_start: 0.7467 (OUTLIER) cc_final: 0.7200 (p) outliers start: 54 outliers final: 21 residues processed: 417 average time/residue: 2.0162 time to fit residues: 953.8686 Evaluate side-chains 414 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 380 time to evaluate : 3.674 ------------------------------------------------------------------------------- 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 359 GLU 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 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 611 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 394 THR Chi-restraints excluded: chain E residue 410 ARG Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 186 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 611 SER Chi-restraints excluded: chain I residue 260 LEU 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 318 ARG Chi-restraints excluded: chain K residue 574 GLU Chi-restraints excluded: chain K residue 640 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 58 optimal weight: 5.9990 chunk 299 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 114 optimal weight: 8.9990 chunk 353 optimal weight: 2.9990 chunk 374 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 176 optimal weight: 9.9990 chunk 198 optimal weight: 0.6980 chunk 96 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- 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 309 ASN E 309 ASN G 309 ASN I 409 GLN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 309 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.135093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.099330 restraints weight = 54669.296| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.68 r_work: 0.2955 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 31320 Z= 0.239 Angle : 0.717 9.181 42516 Z= 0.376 Chirality : 0.049 0.192 4842 Planarity : 0.006 0.055 5580 Dihedral : 5.414 39.998 4354 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.92 % Allowed : 9.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.13), residues: 4062 helix: 0.74 (0.13), residues: 1428 sheet: 0.32 (0.19), residues: 786 loop : -0.59 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 651 HIS 0.005 0.001 HIS B 446 PHE 0.027 0.002 PHE E 595 TYR 0.023 0.003 TYR E 607 ARG 0.006 0.001 ARG K 627 Details of bonding type rmsd hydrogen bonds : bond 0.06115 ( 1198) hydrogen bonds : angle 5.16261 ( 3312) covalent geometry : bond 0.00559 (31320) covalent geometry : angle 0.71687 (42516) *********************** 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 443 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 385 time to evaluate : 3.531 Fit side-chains REVERT: A 205 GLU cc_start: 0.7808 (tp30) cc_final: 0.7553 (tt0) REVERT: A 339 ASN cc_start: 0.7450 (m110) cc_final: 0.7231 (m-40) REVERT: A 384 GLN cc_start: 0.7195 (mm-40) cc_final: 0.6987 (tp40) REVERT: A 410 ARG cc_start: 0.7663 (ttm-80) cc_final: 0.7443 (ttm-80) REVERT: B 73 LYS cc_start: 0.8418 (mttm) cc_final: 0.8156 (mttt) REVERT: B 159 PHE cc_start: 0.8542 (m-80) cc_final: 0.8251 (m-80) REVERT: B 186 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8325 (t) REVERT: B 199 ASP cc_start: 0.8270 (m-30) cc_final: 0.8037 (m-30) REVERT: B 256 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7974 (tm-30) REVERT: B 318 ARG cc_start: 0.7309 (ttt90) cc_final: 0.7082 (ttm170) REVERT: B 359 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7220 (mt-10) REVERT: E 8 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7833 (mp) REVERT: E 20 ARG cc_start: 0.7180 (mtp85) cc_final: 0.6527 (ttm-80) REVERT: E 21 LEU cc_start: 0.8121 (mp) cc_final: 0.7893 (mm) REVERT: E 41 MET cc_start: 0.8354 (mmt) cc_final: 0.7783 (mmm) REVERT: E 46 GLN cc_start: 0.8269 (tp-100) cc_final: 0.7964 (tp40) REVERT: E 81 ARG cc_start: 0.7260 (ttm110) cc_final: 0.6755 (mtm110) REVERT: E 195 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7840 (ttpt) REVERT: E 318 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6123 (tpp-160) REVERT: E 365 GLN cc_start: 0.6910 (tp40) cc_final: 0.6650 (tm-30) REVERT: E 410 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7512 (ttm170) REVERT: E 414 GLN cc_start: 0.8059 (mt0) cc_final: 0.7806 (mt0) REVERT: E 458 LYS cc_start: 0.8085 (tmtp) cc_final: 0.7685 (ttmt) REVERT: E 642 GLU cc_start: 0.5701 (pp20) cc_final: 0.5186 (tm-30) REVERT: G 73 LYS cc_start: 0.8407 (mttm) cc_final: 0.8146 (mttt) REVERT: G 159 PHE cc_start: 0.8560 (m-80) cc_final: 0.8301 (m-80) REVERT: G 186 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8307 (t) REVERT: G 348 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7488 (tm-30) REVERT: G 365 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6769 (mm-40) REVERT: I 20 ARG cc_start: 0.7273 (mtp-110) cc_final: 0.6962 (mtp-110) REVERT: I 37 GLU cc_start: 0.7227 (tt0) cc_final: 0.6748 (mt-10) REVERT: I 359 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7598 (mt-10) REVERT: I 384 GLN cc_start: 0.7374 (mm110) cc_final: 0.6877 (mm-40) REVERT: K 33 GLU cc_start: 0.7867 (tt0) cc_final: 0.7467 (tt0) REVERT: K 41 MET cc_start: 0.8360 (mmt) cc_final: 0.7762 (mmm) REVERT: K 46 GLN cc_start: 0.8112 (tp-100) cc_final: 0.7818 (tp40) REVERT: K 81 ARG cc_start: 0.7298 (ttm110) cc_final: 0.6805 (mtm110) REVERT: K 318 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6135 (tpp-160) REVERT: K 458 LYS cc_start: 0.8110 (tmtp) cc_final: 0.7892 (tttt) outliers start: 58 outliers final: 31 residues processed: 424 average time/residue: 2.0363 time to fit residues: 978.7451 Evaluate side-chains 421 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 378 time to evaluate : 3.391 ------------------------------------------------------------------------------- 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 359 GLU 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 611 SER Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 195 LYS Chi-restraints excluded: chain E residue 196 SER 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 184 THR Chi-restraints excluded: chain G residue 186 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 365 GLN 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 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 196 SER Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 318 ARG Chi-restraints excluded: chain K residue 574 GLU Chi-restraints excluded: chain K residue 640 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 41 optimal weight: 5.9990 chunk 377 optimal weight: 6.9990 chunk 382 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 182 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 232 optimal weight: 0.9980 chunk 236 optimal weight: 10.0000 chunk 228 optimal weight: 5.9990 chunk 385 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 overall best weight: 3.1386 ------------------------------------------------------------------------------- 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 309 ASN E 309 ASN 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 = 0.3607 r_free = 0.3607 target = 0.136288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.099343 restraints weight = 52340.899| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.73 r_work: 0.2977 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.57 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: 0.8485 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31320 Z= 0.160 Angle : 0.619 9.031 42516 Z= 0.323 Chirality : 0.045 0.176 4842 Planarity : 0.005 0.052 5580 Dihedral : 5.091 39.695 4354 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.08 % Allowed : 10.19 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.13), residues: 4062 helix: 1.04 (0.13), residues: 1428 sheet: 0.43 (0.19), residues: 786 loop : -0.48 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 651 HIS 0.005 0.001 HIS I 463 PHE 0.027 0.002 PHE E 595 TYR 0.020 0.002 TYR E 607 ARG 0.006 0.000 ARG I 410 Details of bonding type rmsd hydrogen bonds : bond 0.05023 ( 1198) hydrogen bonds : angle 4.93308 ( 3312) covalent geometry : bond 0.00366 (31320) covalent geometry : angle 0.61882 (42516) *********************** 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 453 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 391 time to evaluate : 3.528 Fit side-chains REVERT: A 33 GLU cc_start: 0.7637 (pp20) cc_final: 0.7401 (pp20) REVERT: A 205 GLU cc_start: 0.7886 (tp30) cc_final: 0.7609 (tt0) REVERT: A 384 GLN cc_start: 0.7176 (mm-40) cc_final: 0.6963 (tp40) REVERT: A 410 ARG cc_start: 0.7653 (ttm-80) cc_final: 0.7438 (ttm-80) REVERT: A 610 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7585 (mm-30) REVERT: B 73 LYS cc_start: 0.8436 (mttm) cc_final: 0.8176 (mttt) REVERT: B 159 PHE cc_start: 0.8509 (m-80) cc_final: 0.8256 (m-80) REVERT: B 186 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8351 (t) REVERT: B 256 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7997 (tm-30) REVERT: B 285 ARG cc_start: 0.8031 (ttp-110) cc_final: 0.7820 (ttp80) REVERT: B 359 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7277 (mt-10) REVERT: E 8 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7784 (mp) REVERT: E 20 ARG cc_start: 0.7047 (mtp85) cc_final: 0.6471 (ttm-80) REVERT: E 33 GLU cc_start: 0.7754 (tt0) cc_final: 0.7392 (tm-30) REVERT: E 81 ARG cc_start: 0.7179 (ttm110) cc_final: 0.6660 (mtm110) REVERT: E 186 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8320 (t) REVERT: E 195 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7975 (ttpt) REVERT: E 318 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.5742 (tpt170) REVERT: E 365 GLN cc_start: 0.6915 (tp40) cc_final: 0.6681 (tm-30) REVERT: E 410 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7442 (ttm170) REVERT: E 414 GLN cc_start: 0.8047 (mt0) cc_final: 0.7770 (mt0) REVERT: G 73 LYS cc_start: 0.8418 (mttm) cc_final: 0.8160 (mttt) REVERT: G 186 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8326 (t) REVERT: G 348 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7465 (tm-30) REVERT: G 610 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7165 (mt-10) REVERT: I 20 ARG cc_start: 0.7353 (mtp-110) cc_final: 0.6535 (ttm-80) REVERT: I 37 GLU cc_start: 0.7184 (tt0) cc_final: 0.6726 (mt-10) REVERT: I 205 GLU cc_start: 0.7701 (tp30) cc_final: 0.7489 (tt0) REVERT: I 348 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7424 (tm-30) REVERT: I 384 GLN cc_start: 0.7324 (mm110) cc_final: 0.6790 (mm-40) REVERT: I 385 PRO cc_start: 0.7687 (Cg_endo) cc_final: 0.7309 (Cg_exo) REVERT: I 521 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7775 (mt-10) REVERT: I 610 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7592 (mm-30) REVERT: K 33 GLU cc_start: 0.7834 (tt0) cc_final: 0.7451 (tt0) REVERT: K 41 MET cc_start: 0.8338 (mmt) cc_final: 0.7746 (mmm) REVERT: K 46 GLN cc_start: 0.8198 (tp-100) cc_final: 0.7971 (tp40) REVERT: K 81 ARG cc_start: 0.7241 (ttm110) cc_final: 0.6761 (mtm110) REVERT: K 186 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8337 (t) REVERT: K 318 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.5810 (tpt170) REVERT: K 458 LYS cc_start: 0.8110 (tmtp) cc_final: 0.7898 (tttt) REVERT: K 640 SER cc_start: 0.7581 (OUTLIER) cc_final: 0.7379 (p) outliers start: 62 outliers final: 24 residues processed: 432 average time/residue: 1.9214 time to fit residues: 943.0374 Evaluate side-chains 420 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 379 time to evaluate : 3.641 ------------------------------------------------------------------------------- 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 576 ILE Chi-restraints excluded: chain A residue 610 GLU 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 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 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 318 ARG 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 186 THR Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 611 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 610 GLU 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 269 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 197 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 183 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 297 optimal weight: 9.9990 chunk 396 optimal weight: 6.9990 chunk 201 optimal weight: 20.0000 chunk 391 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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 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 = 0.3595 r_free = 0.3595 target = 0.135375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.099858 restraints weight = 67548.410| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.99 r_work: 0.2960 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 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 = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 31320 Z= 0.214 Angle : 0.688 10.159 42516 Z= 0.360 Chirality : 0.048 0.189 4842 Planarity : 0.005 0.059 5580 Dihedral : 5.296 40.052 4354 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.42 % Allowed : 10.19 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.13), residues: 4062 helix: 0.91 (0.13), residues: 1428 sheet: 0.43 (0.19), residues: 786 loop : -0.48 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 651 HIS 0.005 0.001 HIS B 446 PHE 0.026 0.002 PHE E 595 TYR 0.022 0.003 TYR B 493 ARG 0.006 0.001 ARG B 81 Details of bonding type rmsd hydrogen bonds : bond 0.05810 ( 1198) hydrogen bonds : angle 5.07601 ( 3312) covalent geometry : bond 0.00497 (31320) covalent geometry : angle 0.68848 (42516) *********************** 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 460 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 387 time to evaluate : 3.475 Fit side-chains REVERT: A 33 GLU cc_start: 0.7642 (pp20) cc_final: 0.7371 (pp20) REVERT: A 81 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6689 (mtm110) REVERT: A 348 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7383 (tm-30) REVERT: A 384 GLN cc_start: 0.7133 (mm-40) cc_final: 0.6933 (tp40) REVERT: A 410 ARG cc_start: 0.7591 (ttm-80) cc_final: 0.7364 (ttm-80) REVERT: B 73 LYS cc_start: 0.8383 (mttm) cc_final: 0.8115 (mttt) REVERT: B 159 PHE cc_start: 0.8522 (m-80) cc_final: 0.8238 (m-80) REVERT: B 186 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8360 (t) REVERT: B 199 ASP cc_start: 0.8253 (m-30) cc_final: 0.8027 (m-30) REVERT: B 256 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.8001 (tm-30) REVERT: B 359 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7194 (mt-10) REVERT: E 8 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7774 (mp) REVERT: E 20 ARG cc_start: 0.7118 (mtp85) cc_final: 0.6451 (ttm-80) REVERT: E 33 GLU cc_start: 0.7823 (tt0) cc_final: 0.7338 (tt0) REVERT: E 81 ARG cc_start: 0.7163 (ttm110) cc_final: 0.6642 (mtm110) REVERT: E 186 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8323 (t) REVERT: E 195 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7762 (ttpt) REVERT: E 318 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.5883 (tpt170) REVERT: E 365 GLN cc_start: 0.6861 (tp40) cc_final: 0.6594 (tm-30) REVERT: E 410 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7431 (ttm170) REVERT: E 414 GLN cc_start: 0.8015 (mt0) cc_final: 0.7759 (mt0) REVERT: G 73 LYS cc_start: 0.8364 (mttm) cc_final: 0.8095 (mttt) REVERT: G 159 PHE cc_start: 0.8536 (m-80) cc_final: 0.8333 (m-80) REVERT: G 186 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8332 (t) REVERT: G 348 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7460 (tm-30) REVERT: I 20 ARG cc_start: 0.7308 (mtp-110) cc_final: 0.6495 (ttm-80) REVERT: I 37 GLU cc_start: 0.7169 (tt0) cc_final: 0.6702 (mt-10) REVERT: I 81 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6743 (mtm110) REVERT: I 205 GLU cc_start: 0.7661 (tp30) cc_final: 0.7440 (tt0) REVERT: I 329 GLN cc_start: 0.5981 (mm-40) cc_final: 0.5741 (mm110) REVERT: I 348 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7379 (tm-30) REVERT: I 384 GLN cc_start: 0.7378 (mm110) cc_final: 0.6775 (mm-40) REVERT: I 385 PRO cc_start: 0.7676 (Cg_endo) cc_final: 0.7321 (Cg_exo) REVERT: K 33 GLU cc_start: 0.7841 (tt0) cc_final: 0.7424 (tt0) REVERT: K 46 GLN cc_start: 0.8111 (tp-100) cc_final: 0.7892 (tp40) REVERT: K 81 ARG cc_start: 0.7146 (ttm110) cc_final: 0.6660 (mtm110) REVERT: K 186 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8333 (t) REVERT: K 318 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.5934 (tpt170) REVERT: K 458 LYS cc_start: 0.8094 (tmtp) cc_final: 0.7886 (tttt) REVERT: K 610 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7436 (mm-30) REVERT: K 640 SER cc_start: 0.7557 (OUTLIER) cc_final: 0.7332 (p) outliers start: 73 outliers final: 31 residues processed: 429 average time/residue: 1.8968 time to fit residues: 932.4850 Evaluate side-chains 427 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 378 time to evaluate : 3.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 348 GLU 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 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 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 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 184 THR Chi-restraints excluded: chain G residue 186 THR 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 611 SER Chi-restraints excluded: chain I residue 81 ARG 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 227 VAL Chi-restraints excluded: chain K residue 269 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 610 GLU Chi-restraints excluded: chain K residue 640 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 296 optimal weight: 9.9990 chunk 309 optimal weight: 20.0000 chunk 179 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 347 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 398 optimal weight: 8.9990 chunk 219 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 160 optimal weight: 20.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 13 GLN B 309 ASN E 309 ASN G 13 GLN G 309 ASN I 191 GLN I 293 GLN I 409 GLN K 3 GLN K 309 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.136949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.099815 restraints weight = 54208.053| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.75 r_work: 0.2981 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1353 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= 0.132 Angle : 0.585 9.036 42516 Z= 0.304 Chirality : 0.044 0.166 4842 Planarity : 0.004 0.050 5580 Dihedral : 4.881 38.471 4354 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.95 % Allowed : 10.97 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.13), residues: 4062 helix: 1.22 (0.13), residues: 1434 sheet: 0.54 (0.19), residues: 786 loop : -0.39 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 651 HIS 0.005 0.001 HIS I 463 PHE 0.027 0.002 PHE E 595 TYR 0.019 0.002 TYR E 607 ARG 0.007 0.000 ARG B 81 Details of bonding type rmsd hydrogen bonds : bond 0.04552 ( 1198) hydrogen bonds : angle 4.80232 ( 3312) covalent geometry : bond 0.00296 (31320) covalent geometry : angle 0.58467 (42516) *********************** 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 452 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 394 time to evaluate : 3.625 Fit side-chains REVERT: A 33 GLU cc_start: 0.7666 (pp20) cc_final: 0.7361 (pp20) REVERT: A 34 VAL cc_start: 0.8121 (t) cc_final: 0.7656 (p) REVERT: A 348 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7418 (tm-30) REVERT: A 410 ARG cc_start: 0.7626 (ttm-80) cc_final: 0.7419 (ttm-80) REVERT: A 521 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7701 (mt-10) REVERT: B 13 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7845 (pt0) REVERT: B 73 LYS cc_start: 0.8433 (mttm) cc_final: 0.8177 (mttt) REVERT: B 186 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8306 (t) REVERT: B 359 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7273 (mt-10) REVERT: E 8 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7758 (mp) REVERT: E 20 ARG cc_start: 0.7126 (mtp85) cc_final: 0.6546 (ttm-80) REVERT: E 33 GLU cc_start: 0.7775 (tt0) cc_final: 0.7411 (tm-30) REVERT: E 41 MET cc_start: 0.8336 (mmt) cc_final: 0.7693 (mmm) REVERT: E 78 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7546 (mt-10) REVERT: E 81 ARG cc_start: 0.7215 (ttm110) cc_final: 0.6699 (mtm110) REVERT: E 186 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8327 (t) REVERT: E 195 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7996 (ttpt) REVERT: E 318 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.5676 (tpt170) REVERT: E 365 GLN cc_start: 0.6920 (tp40) cc_final: 0.6680 (tm-30) REVERT: E 410 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7425 (ttm170) REVERT: E 414 GLN cc_start: 0.8035 (mt0) cc_final: 0.7724 (tt0) REVERT: E 523 ARG cc_start: 0.7457 (ptt-90) cc_final: 0.6949 (ptt180) REVERT: G 13 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7839 (pt0) REVERT: G 33 GLU cc_start: 0.5910 (mt-10) cc_final: 0.5279 (mp0) REVERT: G 73 LYS cc_start: 0.8396 (mttm) cc_final: 0.8135 (mttt) REVERT: G 186 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8309 (t) REVERT: G 294 LYS cc_start: 0.8281 (mtmt) cc_final: 0.8062 (mtmp) REVERT: G 348 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7533 (tm-30) REVERT: G 610 GLU cc_start: 0.7360 (mm-30) cc_final: 0.7103 (mt-10) REVERT: I 20 ARG cc_start: 0.7440 (mtp-110) cc_final: 0.7090 (mmm160) REVERT: I 37 GLU cc_start: 0.7205 (tt0) cc_final: 0.6746 (mt-10) REVERT: I 205 GLU cc_start: 0.7800 (tp30) cc_final: 0.7562 (tt0) REVERT: I 329 GLN cc_start: 0.6042 (mm-40) cc_final: 0.5771 (mm110) REVERT: I 348 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7437 (tm-30) REVERT: I 385 PRO cc_start: 0.7712 (Cg_endo) cc_final: 0.7479 (Cg_exo) REVERT: I 521 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7751 (mt-10) REVERT: K 33 GLU cc_start: 0.7826 (tt0) cc_final: 0.7443 (tm-30) REVERT: K 41 MET cc_start: 0.8353 (mmt) cc_final: 0.7700 (mmm) REVERT: K 46 GLN cc_start: 0.8217 (tp-100) cc_final: 0.7958 (tp40) REVERT: K 78 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7487 (mt-10) REVERT: K 81 ARG cc_start: 0.7213 (ttm110) cc_final: 0.6827 (mtm110) REVERT: K 186 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8342 (t) REVERT: K 318 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.5712 (tpt170) REVERT: K 458 LYS cc_start: 0.8115 (tmtp) cc_final: 0.7909 (tttt) outliers start: 58 outliers final: 19 residues processed: 430 average time/residue: 1.8662 time to fit residues: 911.2131 Evaluate side-chains 407 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 371 time to evaluate : 3.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 348 GLU 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 3 GLN Chi-restraints excluded: chain B residue 13 GLN 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 321 LYS Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 518 LYS 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 410 ARG Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 254 THR 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 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 227 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 271 optimal weight: 9.9990 chunk 391 optimal weight: 7.9990 chunk 267 optimal weight: 5.9990 chunk 252 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 314 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 250 optimal weight: 5.9990 chunk 221 optimal weight: 2.9990 chunk 154 optimal weight: 0.0670 chunk 347 optimal weight: 4.9990 overall best weight: 2.1924 ------------------------------------------------------------------------------- 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 A 329 GLN A 409 GLN B 309 ASN E 309 ASN E 339 ASN G 309 ASN I 293 GLN I 409 GLN K 3 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 = 0.3614 r_free = 0.3614 target = 0.136622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.101477 restraints weight = 56441.569| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.69 r_work: 0.2983 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 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 = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1410 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= 0.132 Angle : 0.588 10.577 42516 Z= 0.304 Chirality : 0.044 0.170 4842 Planarity : 0.004 0.049 5580 Dihedral : 4.828 38.055 4354 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.73 % Allowed : 11.79 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.13), residues: 4062 helix: 1.29 (0.13), residues: 1434 sheet: 0.60 (0.19), residues: 786 loop : -0.31 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 651 HIS 0.005 0.001 HIS I 463 PHE 0.026 0.002 PHE E 595 TYR 0.019 0.002 TYR E 607 ARG 0.008 0.000 ARG B 81 Details of bonding type rmsd hydrogen bonds : bond 0.04519 ( 1198) hydrogen bonds : angle 4.76427 ( 3312) covalent geometry : bond 0.00296 (31320) covalent geometry : angle 0.58756 (42516) *********************** 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 : 3.281 Fit side-chains REVERT: A 33 GLU cc_start: 0.7675 (pp20) cc_final: 0.7404 (pp20) REVERT: A 34 VAL cc_start: 0.8117 (t) cc_final: 0.7661 (p) REVERT: A 348 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7391 (tm-30) REVERT: A 410 ARG cc_start: 0.7636 (ttm-80) cc_final: 0.7425 (ttm-80) REVERT: B 73 LYS cc_start: 0.8433 (mttm) cc_final: 0.8177 (mttt) REVERT: B 186 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8304 (t) REVERT: B 359 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7282 (mt-10) REVERT: B 410 ARG cc_start: 0.7433 (ttm-80) cc_final: 0.6955 (ttp-110) REVERT: E 8 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7732 (mp) REVERT: E 20 ARG cc_start: 0.7145 (mtp85) cc_final: 0.6559 (ttm-80) REVERT: E 33 GLU cc_start: 0.7708 (tt0) cc_final: 0.7313 (tm-30) REVERT: E 78 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7573 (mt-10) REVERT: E 81 ARG cc_start: 0.7195 (ttm110) cc_final: 0.6828 (mtm110) REVERT: E 195 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8029 (ttpt) REVERT: E 318 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.5694 (tpt170) REVERT: E 365 GLN cc_start: 0.6871 (tp40) cc_final: 0.6637 (tm-30) REVERT: E 410 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7453 (ttm170) REVERT: E 414 GLN cc_start: 0.8024 (mt0) cc_final: 0.7721 (tt0) REVERT: E 458 LYS cc_start: 0.8256 (tttt) cc_final: 0.8025 (ttmt) REVERT: E 523 ARG cc_start: 0.7456 (ptt-90) cc_final: 0.6951 (ptt180) REVERT: E 642 GLU cc_start: 0.5484 (pm20) cc_final: 0.5202 (pp20) REVERT: G 33 GLU cc_start: 0.5883 (mt-10) cc_final: 0.5251 (mp0) REVERT: G 73 LYS cc_start: 0.8400 (mttm) cc_final: 0.8140 (mttt) REVERT: G 186 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8311 (t) REVERT: G 294 LYS cc_start: 0.8352 (mtmt) cc_final: 0.8114 (mtmp) REVERT: G 610 GLU cc_start: 0.7264 (mm-30) cc_final: 0.6991 (mt-10) REVERT: I 20 ARG cc_start: 0.7436 (mtp-110) cc_final: 0.7111 (mmm160) REVERT: I 37 GLU cc_start: 0.7208 (tt0) cc_final: 0.6746 (mt-10) REVERT: I 205 GLU cc_start: 0.7846 (tp30) cc_final: 0.7611 (tt0) REVERT: I 329 GLN cc_start: 0.5978 (mm-40) cc_final: 0.5684 (mm110) REVERT: I 348 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7423 (tm-30) REVERT: I 385 PRO cc_start: 0.7692 (Cg_endo) cc_final: 0.7464 (Cg_exo) REVERT: K 8 LEU cc_start: 0.8235 (pp) cc_final: 0.8017 (pp) REVERT: K 33 GLU cc_start: 0.7785 (tt0) cc_final: 0.7421 (tt0) REVERT: K 46 GLN cc_start: 0.8176 (tp-100) cc_final: 0.7945 (tp40) REVERT: K 78 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7530 (mt-10) REVERT: K 81 ARG cc_start: 0.7201 (ttm110) cc_final: 0.6842 (mtm110) REVERT: K 305 GLN cc_start: 0.7939 (tp-100) cc_final: 0.7448 (tp40) REVERT: K 318 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.5760 (tpt170) REVERT: K 458 LYS cc_start: 0.8115 (tmtp) cc_final: 0.7906 (tttt) REVERT: K 610 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7512 (mm-30) outliers start: 51 outliers final: 21 residues processed: 412 average time/residue: 2.0615 time to fit residues: 972.2204 Evaluate side-chains 402 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 370 time to evaluate : 3.782 ------------------------------------------------------------------------------- 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 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 193 MET Chi-restraints excluded: chain B residue 254 THR 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 195 LYS Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 410 ARG Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 518 LYS 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 227 VAL Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain K residue 318 ARG Chi-restraints excluded: chain K residue 540 LEU Chi-restraints excluded: chain K residue 610 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 185 optimal weight: 7.9990 chunk 233 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 335 optimal weight: 20.0000 chunk 161 optimal weight: 0.0020 chunk 184 optimal weight: 2.9990 chunk 374 optimal weight: 0.6980 chunk 118 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 overall best weight: 2.7394 ------------------------------------------------------------------------------- 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 B 46 GLN B 309 ASN E 309 ASN E 339 ASN G 13 GLN G 309 ASN I 293 GLN I 409 GLN K 3 GLN K 309 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.100894 restraints weight = 60128.019| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.07 r_work: 0.2985 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 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 = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31320 Z= 0.148 Angle : 0.608 10.601 42516 Z= 0.314 Chirality : 0.045 0.172 4842 Planarity : 0.004 0.050 5580 Dihedral : 4.902 37.912 4354 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.51 % Allowed : 12.04 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.13), residues: 4062 helix: 1.24 (0.13), residues: 1434 sheet: 0.61 (0.19), residues: 786 loop : -0.30 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 651 HIS 0.005 0.001 HIS I 463 PHE 0.026 0.002 PHE E 595 TYR 0.020 0.002 TYR K 607 ARG 0.008 0.000 ARG G 81 Details of bonding type rmsd hydrogen bonds : bond 0.04773 ( 1198) hydrogen bonds : angle 4.80451 ( 3312) covalent geometry : bond 0.00335 (31320) covalent geometry : angle 0.60784 (42516) *********************** 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 423 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 379 time to evaluate : 3.794 Fit side-chains REVERT: A 20 ARG cc_start: 0.7123 (mtp85) cc_final: 0.6892 (mmm160) REVERT: A 33 GLU cc_start: 0.7651 (pp20) cc_final: 0.7382 (pp20) REVERT: A 329 GLN cc_start: 0.6054 (mt0) cc_final: 0.5337 (mm-40) REVERT: A 348 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7380 (tm-30) REVERT: A 410 ARG cc_start: 0.7612 (ttm-80) cc_final: 0.7398 (ttm-80) REVERT: A 521 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: B 73 LYS cc_start: 0.8423 (mttm) cc_final: 0.8162 (mttt) REVERT: B 186 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8299 (t) REVERT: B 359 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7242 (mt-10) REVERT: E 8 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7705 (mp) REVERT: E 20 ARG cc_start: 0.7134 (mtp85) cc_final: 0.6550 (ttm-80) REVERT: E 33 GLU cc_start: 0.7691 (tt0) cc_final: 0.7293 (tm-30) REVERT: E 78 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7550 (mt-10) REVERT: E 81 ARG cc_start: 0.7161 (ttm110) cc_final: 0.6794 (mtm110) REVERT: E 195 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7980 (ttpt) REVERT: E 256 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.8030 (tt0) REVERT: E 318 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.5752 (tpt170) REVERT: E 365 GLN cc_start: 0.6868 (tp40) cc_final: 0.6608 (tm-30) REVERT: E 410 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7416 (ttm170) REVERT: E 414 GLN cc_start: 0.8004 (mt0) cc_final: 0.7691 (tt0) REVERT: G 33 GLU cc_start: 0.5855 (mt-10) cc_final: 0.5209 (mp0) REVERT: G 73 LYS cc_start: 0.8386 (mttm) cc_final: 0.8120 (mttt) REVERT: G 186 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8308 (t) REVERT: G 294 LYS cc_start: 0.8326 (mtmt) cc_final: 0.8096 (mtmp) REVERT: G 610 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6976 (mt-10) REVERT: I 20 ARG cc_start: 0.7409 (mtp-110) cc_final: 0.7054 (mmm160) REVERT: I 37 GLU cc_start: 0.7192 (tt0) cc_final: 0.6751 (mt-10) REVERT: I 205 GLU cc_start: 0.7798 (tp30) cc_final: 0.7567 (tt0) REVERT: I 329 GLN cc_start: 0.5926 (mm-40) cc_final: 0.5645 (mm110) REVERT: I 348 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7433 (tm-30) REVERT: I 385 PRO cc_start: 0.7695 (Cg_endo) cc_final: 0.7447 (Cg_exo) REVERT: K 33 GLU cc_start: 0.7775 (tt0) cc_final: 0.7411 (tt0) REVERT: K 46 GLN cc_start: 0.8186 (tp-100) cc_final: 0.7923 (tp40) REVERT: K 78 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7508 (mt-10) REVERT: K 81 ARG cc_start: 0.7160 (ttm110) cc_final: 0.6802 (mtm110) REVERT: K 305 GLN cc_start: 0.7933 (tp-100) cc_final: 0.7435 (tp40) REVERT: K 318 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.5796 (tpt170) REVERT: K 458 LYS cc_start: 0.8097 (tmtp) cc_final: 0.7889 (tttt) REVERT: K 523 ARG cc_start: 0.7499 (mtm180) cc_final: 0.7053 (ptt-90) REVERT: K 574 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7917 (pt0) REVERT: K 610 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7460 (mm-30) outliers start: 44 outliers final: 22 residues processed: 407 average time/residue: 1.9120 time to fit residues: 883.3857 Evaluate side-chains 409 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 373 time to evaluate : 3.307 ------------------------------------------------------------------------------- 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 521 GLU 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 193 MET Chi-restraints excluded: chain B residue 254 THR 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 195 LYS Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 410 ARG Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 186 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 518 LYS 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 269 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 610 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 373 optimal weight: 7.9990 chunk 271 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 372 optimal weight: 10.0000 chunk 230 optimal weight: 0.0050 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 27 optimal weight: 0.0040 chunk 62 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 376 optimal weight: 5.9990 overall best weight: 3.2012 ------------------------------------------------------------------------------- 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 13 GLN B 46 GLN B 309 ASN E 309 ASN E 339 ASN G 13 GLN G 46 GLN G 309 ASN I 293 GLN I 409 GLN K 3 GLN K 309 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.136264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.101228 restraints weight = 58206.988| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.79 r_work: 0.2967 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 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 = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 31320 Z= 0.161 Angle : 0.625 10.669 42516 Z= 0.324 Chirality : 0.045 0.176 4842 Planarity : 0.005 0.051 5580 Dihedral : 4.965 37.938 4354 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.54 % Allowed : 12.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.13), residues: 4062 helix: 1.19 (0.13), residues: 1434 sheet: 0.60 (0.19), residues: 786 loop : -0.30 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 651 HIS 0.005 0.001 HIS I 463 PHE 0.026 0.002 PHE E 595 TYR 0.020 0.002 TYR K 607 ARG 0.008 0.001 ARG B 81 Details of bonding type rmsd hydrogen bonds : bond 0.04963 ( 1198) hydrogen bonds : angle 4.84494 ( 3312) covalent geometry : bond 0.00369 (31320) covalent geometry : angle 0.62465 (42516) ********************** 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 417 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 372 time to evaluate : 4.564 Fit side-chains REVERT: A 33 GLU cc_start: 0.7719 (pp20) cc_final: 0.7453 (pp20) REVERT: A 329 GLN cc_start: 0.5997 (mt0) cc_final: 0.5277 (mm-40) REVERT: A 348 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7431 (tm-30) REVERT: A 410 ARG cc_start: 0.7656 (ttm-80) cc_final: 0.7438 (ttm-80) REVERT: A 521 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7793 (mt-10) REVERT: B 73 LYS cc_start: 0.8443 (mttm) cc_final: 0.8186 (mttt) REVERT: B 186 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8318 (t) REVERT: B 359 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7271 (mt-10) REVERT: E 8 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7771 (mp) REVERT: E 20 ARG cc_start: 0.7171 (mtp85) cc_final: 0.6589 (ttm-80) REVERT: E 33 GLU cc_start: 0.7740 (tt0) cc_final: 0.7354 (tt0) REVERT: E 78 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7571 (mt-10) REVERT: E 81 ARG cc_start: 0.7205 (ttm110) cc_final: 0.6836 (mtm110) REVERT: E 195 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8025 (ttpt) REVERT: E 318 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.5800 (tpt170) REVERT: E 365 GLN cc_start: 0.6876 (tp40) cc_final: 0.6634 (tm-30) REVERT: E 410 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7480 (ttm170) REVERT: E 414 GLN cc_start: 0.8054 (mt0) cc_final: 0.7747 (tt0) REVERT: G 13 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8029 (pt0) REVERT: G 33 GLU cc_start: 0.5921 (mt-10) cc_final: 0.5211 (mp0) REVERT: G 73 LYS cc_start: 0.8411 (mttm) cc_final: 0.8149 (mttt) REVERT: G 186 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8320 (t) REVERT: G 294 LYS cc_start: 0.8365 (mtmt) cc_final: 0.8144 (mtmp) REVERT: I 20 ARG cc_start: 0.7442 (mtp-110) cc_final: 0.7094 (mmm160) REVERT: I 37 GLU cc_start: 0.7235 (tt0) cc_final: 0.6773 (mt-10) REVERT: I 205 GLU cc_start: 0.7856 (tp30) cc_final: 0.7612 (tt0) REVERT: I 329 GLN cc_start: 0.5982 (mm-40) cc_final: 0.5696 (mm110) REVERT: I 348 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7492 (tm-30) REVERT: I 385 PRO cc_start: 0.7703 (Cg_endo) cc_final: 0.7443 (Cg_exo) REVERT: K 33 GLU cc_start: 0.7857 (tt0) cc_final: 0.7500 (tt0) REVERT: K 46 GLN cc_start: 0.8163 (tp-100) cc_final: 0.7868 (tp40) REVERT: K 78 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7595 (mt-10) REVERT: K 81 ARG cc_start: 0.7209 (ttm110) cc_final: 0.6847 (mtm110) REVERT: K 318 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.5865 (tpt170) REVERT: K 458 LYS cc_start: 0.8120 (tmtp) cc_final: 0.7913 (tttt) REVERT: K 523 ARG cc_start: 0.7477 (mtm180) cc_final: 0.7099 (ptt-90) REVERT: K 574 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7963 (pt0) REVERT: K 610 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7518 (mm-30) outliers start: 45 outliers final: 22 residues processed: 400 average time/residue: 1.9676 time to fit residues: 896.8177 Evaluate side-chains 408 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 372 time to evaluate : 3.662 ------------------------------------------------------------------------------- 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 521 GLU 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 193 MET Chi-restraints excluded: chain B residue 254 THR 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 195 LYS Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 410 ARG Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 186 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 518 LYS 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 269 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 610 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 200 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 334 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 370 optimal weight: 0.4980 chunk 348 optimal weight: 0.0070 chunk 43 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 326 optimal weight: 10.0000 overall best weight: 1.3004 ------------------------------------------------------------------------------- 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 E 339 ASN G 46 GLN G 309 ASN I 293 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 = 0.3609 r_free = 0.3609 target = 0.136353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.100996 restraints weight = 65325.594| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.34 r_work: 0.2970 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 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 = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.228 31320 Z= 0.173 Angle : 0.747 59.110 42516 Z= 0.415 Chirality : 0.048 1.323 4842 Planarity : 0.005 0.051 5580 Dihedral : 4.955 37.959 4354 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.42 % Allowed : 12.36 % Favored : 86.23 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.13), residues: 4062 helix: 1.20 (0.13), residues: 1434 sheet: 0.61 (0.19), residues: 786 loop : -0.30 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 651 HIS 0.004 0.001 HIS I 463 PHE 0.026 0.002 PHE E 595 TYR 0.021 0.002 TYR K 607 ARG 0.007 0.000 ARG B 81 Details of bonding type rmsd hydrogen bonds : bond 0.04932 ( 1198) hydrogen bonds : angle 4.85243 ( 3312) covalent geometry : bond 0.00387 (31320) covalent geometry : angle 0.74678 (42516) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 36572.84 seconds wall clock time: 626 minutes 49.40 seconds (37609.40 seconds total)