Starting phenix.real_space_refine on Wed May 28 10:39:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wv6_37866/05_2025/8wv6_37866.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wv6_37866/05_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_37866/05_2025/8wv6_37866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wv6_37866/05_2025/8wv6_37866.map" model { file = "/net/cci-nas-00/data/ceres_data/8wv6_37866/05_2025/8wv6_37866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wv6_37866/05_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-5687/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: 29.80, per 1000 atoms: 0.96 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: 7.63 Conformation dependent library (CDL) restraints added in 7.5 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: 3.76 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: 10.54 Time building geometry restraints manager: 8.75 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: 0.05 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: 0.010 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.100 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 82.120 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.390 ------------------------------------------------------------------------------- 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 : 3.322 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: 1.8908 time to fit residues: 1052.4998 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 : 3.349 ------------------------------------------------------------------------------- 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 = 59002.409| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.98 r_work: 0.2953 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2829 ------------------------------------------------------------------------------- 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 : 3.608 Fit side-chains REVERT: A 8 LEU cc_start: 0.8116 (pp) cc_final: 0.7904 (mt) REVERT: A 339 ASN cc_start: 0.7418 (m110) cc_final: 0.7153 (m-40) REVERT: A 384 GLN cc_start: 0.7145 (mm-40) cc_final: 0.6831 (mp10) REVERT: A 410 ARG cc_start: 0.7642 (ttm-80) cc_final: 0.7425 (ttm-80) REVERT: A 521 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7841 (mt-10) REVERT: B 73 LYS cc_start: 0.8422 (mttm) cc_final: 0.8161 (mttt) REVERT: B 159 PHE cc_start: 0.8484 (m-80) cc_final: 0.8254 (m-80) REVERT: B 256 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7991 (tm-30) REVERT: B 318 ARG cc_start: 0.7283 (ttt90) cc_final: 0.6965 (ttm170) REVERT: B 359 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.6927 (mt-10) REVERT: E 20 ARG cc_start: 0.7109 (mtp85) cc_final: 0.6527 (ttm-80) REVERT: E 21 LEU cc_start: 0.8260 (mp) cc_final: 0.8026 (mm) REVERT: E 41 MET cc_start: 0.8347 (mmt) cc_final: 0.7773 (mmm) REVERT: E 46 GLN cc_start: 0.8271 (tp-100) cc_final: 0.8020 (tp40) REVERT: E 81 ARG cc_start: 0.7269 (ttm110) cc_final: 0.6740 (mtm110) REVERT: E 318 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6132 (tpp-160) REVERT: E 365 GLN cc_start: 0.6920 (tp40) cc_final: 0.6627 (tm-30) REVERT: E 414 GLN cc_start: 0.8058 (mt0) cc_final: 0.7818 (mt0) REVERT: G 73 LYS cc_start: 0.8424 (mttm) cc_final: 0.8160 (mttt) REVERT: G 159 PHE cc_start: 0.8504 (m-80) cc_final: 0.8270 (m-80) REVERT: G 199 ASP cc_start: 0.8279 (m-30) cc_final: 0.8047 (m-30) REVERT: I 20 ARG cc_start: 0.7336 (mtp-110) cc_final: 0.7095 (mtp-110) REVERT: I 37 GLU cc_start: 0.7120 (tt0) cc_final: 0.6625 (mt-10) REVERT: I 384 GLN cc_start: 0.7225 (mm110) cc_final: 0.6696 (mm-40) REVERT: I 521 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7875 (mt-10) REVERT: K 8 LEU cc_start: 0.8174 (pp) cc_final: 0.7824 (mp) REVERT: K 33 GLU cc_start: 0.7879 (tt0) cc_final: 0.7476 (tt0) REVERT: K 41 MET cc_start: 0.8384 (mmt) cc_final: 0.7768 (mmm) REVERT: K 46 GLN cc_start: 0.8212 (tp-100) cc_final: 0.7989 (tp40) REVERT: K 73 LYS cc_start: 0.8278 (mttt) cc_final: 0.8010 (mttp) REVERT: K 81 ARG cc_start: 0.7282 (ttm110) cc_final: 0.6778 (mtm110) REVERT: K 318 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.6237 (tpp-160) REVERT: K 414 GLN cc_start: 0.8069 (mt0) cc_final: 0.7854 (mt0) REVERT: K 458 LYS cc_start: 0.8264 (tmtp) cc_final: 0.7984 (tttt) outliers start: 36 outliers final: 14 residues processed: 418 average time/residue: 1.8758 time to fit residues: 889.9102 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 : 3.374 ------------------------------------------------------------------------------- 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: 9.9990 chunk 390 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 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: 2.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.135376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.098943 restraints weight = 46959.791| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.62 r_work: 0.2957 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.0973 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= 0.216 Angle : 0.694 8.657 42516 Z= 0.363 Chirality : 0.048 0.188 4842 Planarity : 0.005 0.059 5580 Dihedral : 5.364 39.891 4354 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.82 % Allowed : 8.90 % 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: -0.11 (0.12), residues: 4062 helix: 0.57 (0.13), residues: 1464 sheet: 0.29 (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 0.05937 ( 1198) hydrogen bonds : angle 5.12913 ( 3312) covalent geometry : bond 0.00501 (31320) covalent geometry : angle 0.69424 (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 443 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 388 time to evaluate : 3.605 Fit side-chains REVERT: A 205 GLU cc_start: 0.7837 (tp30) cc_final: 0.7587 (tt0) REVERT: A 339 ASN cc_start: 0.7428 (m110) cc_final: 0.7203 (m-40) REVERT: A 384 GLN cc_start: 0.7175 (mm-40) cc_final: 0.6854 (mp10) REVERT: A 410 ARG cc_start: 0.7647 (ttm-80) cc_final: 0.7423 (ttm-80) REVERT: B 73 LYS cc_start: 0.8419 (mttm) cc_final: 0.8158 (mttt) REVERT: B 159 PHE cc_start: 0.8531 (m-80) cc_final: 0.8288 (m-80) REVERT: B 186 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8359 (t) REVERT: B 256 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.8003 (tm-30) REVERT: B 318 ARG cc_start: 0.7245 (ttt90) cc_final: 0.6954 (ttm170) REVERT: B 359 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7259 (mt-10) REVERT: E 8 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7808 (mp) REVERT: E 20 ARG cc_start: 0.7145 (mtp85) cc_final: 0.6572 (ttm-80) REVERT: E 21 LEU cc_start: 0.8230 (mp) cc_final: 0.8022 (mm) REVERT: E 41 MET cc_start: 0.8353 (mmt) cc_final: 0.7779 (mmm) REVERT: E 46 GLN cc_start: 0.8203 (tp-100) cc_final: 0.7961 (tp40) REVERT: E 81 ARG cc_start: 0.7228 (ttm110) cc_final: 0.6732 (mtm110) REVERT: E 186 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8315 (t) REVERT: E 195 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7819 (ttpt) REVERT: E 318 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.5915 (tpt170) REVERT: E 365 GLN cc_start: 0.6887 (tp40) cc_final: 0.6618 (tm-30) REVERT: E 410 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7521 (ttm170) REVERT: E 414 GLN cc_start: 0.8068 (mt0) cc_final: 0.7829 (mt0) REVERT: E 458 LYS cc_start: 0.8199 (tmtp) cc_final: 0.7738 (ttmt) REVERT: G 73 LYS cc_start: 0.8421 (mttm) cc_final: 0.8156 (mttt) REVERT: G 159 PHE cc_start: 0.8550 (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: 0.8263 (m-30) cc_final: 0.8026 (m-30) REVERT: I 20 ARG cc_start: 0.7269 (mtp-110) cc_final: 0.6973 (mtp-110) REVERT: I 37 GLU cc_start: 0.7218 (tt0) cc_final: 0.6750 (mt-10) REVERT: I 205 GLU cc_start: 0.7829 (tp30) cc_final: 0.7587 (tt0) REVERT: I 359 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7682 (mt-10) REVERT: I 384 GLN cc_start: 0.7346 (mm110) cc_final: 0.6815 (mm-40) REVERT: K 33 GLU cc_start: 0.7862 (tt0) cc_final: 0.7465 (tt0) REVERT: K 41 MET cc_start: 0.8371 (mmt) cc_final: 0.7758 (mmm) REVERT: K 81 ARG cc_start: 0.7243 (ttm110) cc_final: 0.6757 (mtm110) REVERT: K 186 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8319 (t) REVERT: K 318 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.5937 (tpt170) REVERT: K 458 LYS cc_start: 0.8219 (tmtp) cc_final: 0.7929 (tttt) REVERT: K 640 SER cc_start: 0.7340 (OUTLIER) cc_final: 0.7099 (p) outliers start: 55 outliers final: 22 residues processed: 420 average time/residue: 1.9581 time to fit residues: 934.8285 Evaluate side-chains 417 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 382 time to evaluate : 3.323 ------------------------------------------------------------------------------- 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 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 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: 9.9990 chunk 114 optimal weight: 7.9990 chunk 353 optimal weight: 2.9990 chunk 374 optimal weight: 8.9990 chunk 141 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 198 optimal weight: 0.8980 chunk 96 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 K 46 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 = 0.3601 r_free = 0.3601 target = 0.135839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.099853 restraints weight = 55705.705| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.68 r_work: 0.2963 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 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 = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 31320 Z= 0.187 Angle : 0.653 8.195 42516 Z= 0.342 Chirality : 0.047 0.181 4842 Planarity : 0.005 0.053 5580 Dihedral : 5.230 39.761 4354 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.57 % Allowed : 10.25 % Favored : 88.18 % 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: 0.18 (0.13), residues: 4062 helix: 0.90 (0.13), residues: 1428 sheet: 0.38 (0.19), residues: 786 loop : -0.55 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 651 HIS 0.005 0.001 HIS A 463 PHE 0.027 0.002 PHE E 595 TYR 0.022 0.003 TYR K 607 ARG 0.005 0.001 ARG I 410 Details of bonding type rmsd hydrogen bonds : bond 0.05469 ( 1198) hydrogen bonds : angle 5.02516 ( 3312) covalent geometry : bond 0.00431 (31320) covalent geometry : angle 0.65251 (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 431 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 384 time to evaluate : 3.288 Fit side-chains REVERT: A 205 GLU cc_start: 0.7818 (tp30) cc_final: 0.7552 (tt0) REVERT: A 384 GLN cc_start: 0.7178 (mm-40) cc_final: 0.6971 (tp40) REVERT: A 410 ARG cc_start: 0.7674 (ttm-80) cc_final: 0.7456 (ttm-80) REVERT: B 73 LYS cc_start: 0.8411 (mttm) cc_final: 0.8153 (mttt) REVERT: B 159 PHE cc_start: 0.8522 (m-80) cc_final: 0.8265 (m-80) REVERT: B 186 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8341 (t) REVERT: B 256 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.8007 (tm-30) REVERT: B 318 ARG cc_start: 0.7293 (ttt90) cc_final: 0.7068 (ttm170) REVERT: B 359 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7228 (mt-10) REVERT: E 8 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7810 (mp) REVERT: E 20 ARG cc_start: 0.7017 (mtp85) cc_final: 0.6449 (ttm-80) REVERT: E 41 MET cc_start: 0.8346 (mmt) cc_final: 0.7773 (mmm) REVERT: E 46 GLN cc_start: 0.8290 (tp-100) cc_final: 0.8050 (tp40) REVERT: E 81 ARG cc_start: 0.7188 (ttm110) cc_final: 0.6684 (mtm110) REVERT: E 195 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7863 (ttpt) REVERT: E 318 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.5892 (tpt170) REVERT: E 365 GLN cc_start: 0.6896 (tp40) cc_final: 0.6635 (tm-30) REVERT: E 410 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7481 (ttm170) REVERT: E 414 GLN cc_start: 0.8029 (mt0) cc_final: 0.7762 (mt0) REVERT: E 458 LYS cc_start: 0.8101 (tmtp) cc_final: 0.7705 (ttmt) REVERT: G 73 LYS cc_start: 0.8398 (mttm) cc_final: 0.8142 (mttt) REVERT: G 159 PHE cc_start: 0.8518 (m-80) cc_final: 0.8274 (m-80) REVERT: G 186 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8302 (t) REVERT: G 199 ASP cc_start: 0.8252 (m-30) cc_final: 0.8024 (m-30) REVERT: G 348 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7526 (tm-30) REVERT: I 20 ARG cc_start: 0.7252 (mtp-110) cc_final: 0.6933 (mtp-110) REVERT: I 37 GLU cc_start: 0.7214 (tt0) cc_final: 0.6768 (mt-10) REVERT: I 205 GLU cc_start: 0.7813 (tp30) cc_final: 0.7556 (tt0) REVERT: I 359 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: I 384 GLN cc_start: 0.7384 (mm110) cc_final: 0.6870 (mm-40) REVERT: K 33 GLU cc_start: 0.7846 (tt0) cc_final: 0.7466 (tt0) REVERT: K 41 MET cc_start: 0.8348 (mmt) cc_final: 0.7747 (mmm) REVERT: K 81 ARG cc_start: 0.7229 (ttm110) cc_final: 0.6740 (mtm110) REVERT: K 318 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.5930 (tpt170) REVERT: K 458 LYS cc_start: 0.8099 (tmtp) cc_final: 0.7879 (tttt) outliers start: 47 outliers final: 22 residues processed: 415 average time/residue: 1.9068 time to fit residues: 897.8390 Evaluate side-chains 408 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 375 time to evaluate : 3.351 ------------------------------------------------------------------------------- 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 256 GLU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 518 LYS Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 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 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 I residue 260 LEU Chi-restraints excluded: chain I residue 359 GLU Chi-restraints excluded: chain I residue 574 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 41 optimal weight: 10.0000 chunk 377 optimal weight: 10.0000 chunk 382 optimal weight: 0.9990 chunk 145 optimal weight: 0.4980 chunk 182 optimal weight: 0.0670 chunk 127 optimal weight: 8.9990 chunk 232 optimal weight: 8.9990 chunk 236 optimal weight: 10.0000 chunk 228 optimal weight: 6.9990 chunk 385 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 overall best weight: 1.3124 ------------------------------------------------------------------------------- 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 309 ASN E 309 ASN G 13 GLN G 309 ASN I 293 GLN I 409 GLN K 3 GLN K 46 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 = 0.3628 r_free = 0.3628 target = 0.137792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.101263 restraints weight = 54238.052| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.73 r_work: 0.3007 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 31320 Z= 0.109 Angle : 0.544 9.230 42516 Z= 0.282 Chirality : 0.043 0.160 4842 Planarity : 0.004 0.046 5580 Dihedral : 4.678 37.904 4354 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.76 % Allowed : 10.38 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.38 (0.14), residues: 1428 sheet: 0.49 (0.19), residues: 780 loop : -0.37 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 651 HIS 0.006 0.001 HIS I 463 PHE 0.026 0.002 PHE E 595 TYR 0.020 0.002 TYR K 607 ARG 0.004 0.000 ARG I 410 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 1198) hydrogen bonds : angle 4.67884 ( 3312) covalent geometry : bond 0.00236 (31320) covalent geometry : angle 0.54384 (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 471 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 418 time to evaluate : 3.529 Fit side-chains REVERT: A 20 ARG cc_start: 0.7268 (mtp85) cc_final: 0.7045 (mmm160) REVERT: A 205 GLU cc_start: 0.7897 (tp30) cc_final: 0.7617 (tt0) REVERT: A 410 ARG cc_start: 0.7601 (ttm-80) cc_final: 0.7392 (ttm-80) REVERT: B 13 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7869 (pt0) REVERT: B 73 LYS cc_start: 0.8394 (mttm) cc_final: 0.8137 (mttt) REVERT: B 159 PHE cc_start: 0.8476 (m-80) cc_final: 0.8265 (m-80) REVERT: B 186 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8248 (t) REVERT: B 318 ARG cc_start: 0.7315 (ttt90) cc_final: 0.7102 (ttm170) REVERT: B 359 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7266 (mt-10) REVERT: B 389 PRO cc_start: 0.8326 (Cg_endo) cc_final: 0.8114 (Cg_exo) REVERT: E 20 ARG cc_start: 0.7094 (mtp85) cc_final: 0.6492 (ttm-80) REVERT: E 33 GLU cc_start: 0.7784 (tt0) cc_final: 0.7416 (tm-30) REVERT: E 41 MET cc_start: 0.8333 (mmt) cc_final: 0.7748 (mmm) REVERT: E 78 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7480 (mt-10) REVERT: E 81 ARG cc_start: 0.7149 (ttm110) cc_final: 0.6656 (mtm110) REVERT: E 186 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8309 (t) REVERT: E 365 GLN cc_start: 0.6908 (tp40) cc_final: 0.6673 (tm-30) REVERT: E 414 GLN cc_start: 0.8013 (mt0) cc_final: 0.7741 (mt0) REVERT: E 523 ARG cc_start: 0.7395 (ptt-90) cc_final: 0.6885 (ptt180) REVERT: G 13 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.7825 (pt0) REVERT: G 73 LYS cc_start: 0.8361 (mttm) cc_final: 0.8105 (mttt) REVERT: G 186 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8245 (t) REVERT: G 199 ASP cc_start: 0.8270 (m-30) cc_final: 0.8019 (m-30) REVERT: G 365 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.6722 (mm-40) REVERT: G 610 GLU cc_start: 0.7281 (mm-30) cc_final: 0.7077 (mt-10) REVERT: I 3 GLN cc_start: 0.6909 (OUTLIER) cc_final: 0.6543 (mt0) REVERT: I 20 ARG cc_start: 0.7259 (mtp-110) cc_final: 0.7018 (mmm160) REVERT: I 37 GLU cc_start: 0.7034 (tt0) cc_final: 0.6714 (mt-10) REVERT: I 205 GLU cc_start: 0.7908 (tp30) cc_final: 0.7628 (tt0) REVERT: I 348 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7373 (tm-30) REVERT: I 384 GLN cc_start: 0.7290 (mm110) cc_final: 0.7040 (tp40) REVERT: I 385 PRO cc_start: 0.7667 (Cg_endo) cc_final: 0.7326 (Cg_exo) REVERT: I 521 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: K 33 GLU cc_start: 0.7825 (tt0) cc_final: 0.7407 (tm-30) REVERT: K 41 MET cc_start: 0.8349 (mmt) cc_final: 0.7746 (mmm) REVERT: K 78 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7423 (mt-10) REVERT: K 81 ARG cc_start: 0.7212 (ttm110) cc_final: 0.6823 (mtm110) REVERT: K 186 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8320 (t) REVERT: K 318 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.5696 (tpt170) REVERT: K 458 LYS cc_start: 0.8112 (tmtp) cc_final: 0.7897 (tttt) outliers start: 53 outliers final: 15 residues processed: 454 average time/residue: 1.8353 time to fit residues: 949.0253 Evaluate side-chains 402 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 375 time to evaluate : 3.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 610 GLU Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 365 GLN Chi-restraints excluded: chain I residue 3 GLN 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 523 ARG 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=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: 10.0000 chunk 261 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 297 optimal weight: 6.9990 chunk 396 optimal weight: 9.9990 chunk 201 optimal weight: 20.0000 chunk 391 optimal weight: 8.9990 overall best weight: 4.3786 ------------------------------------------------------------------------------- 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 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 ASN E 309 ASN E 339 ASN ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 309 ASN I 191 GLN I 409 GLN K 3 GLN K 46 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 = 0.3597 r_free = 0.3597 target = 0.135511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.100088 restraints weight = 68954.340| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.94 r_work: 0.2962 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- 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 = 0.44 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: 0.8473 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 31320 Z= 0.200 Angle : 0.668 10.291 42516 Z= 0.347 Chirality : 0.047 0.184 4842 Planarity : 0.005 0.056 5580 Dihedral : 5.174 39.118 4354 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.01 % Allowed : 10.69 % Favored : 87.30 % 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: 0.40 (0.13), residues: 4062 helix: 1.07 (0.13), residues: 1428 sheet: 0.53 (0.19), residues: 786 loop : -0.41 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 651 HIS 0.005 0.001 HIS G 583 PHE 0.025 0.002 PHE I 595 TYR 0.021 0.003 TYR B 493 ARG 0.006 0.001 ARG B 81 Details of bonding type rmsd hydrogen bonds : bond 0.05595 ( 1198) hydrogen bonds : angle 4.98991 ( 3312) covalent geometry : bond 0.00463 (31320) covalent geometry : angle 0.66792 (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 443 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 383 time to evaluate : 3.390 Fit side-chains REVERT: A 33 GLU cc_start: 0.7647 (pp20) cc_final: 0.7428 (pp20) REVERT: A 348 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: A 384 GLN cc_start: 0.7133 (mm-40) cc_final: 0.6800 (mp10) REVERT: A 410 ARG cc_start: 0.7612 (ttm-80) cc_final: 0.7393 (ttm-80) REVERT: B 73 LYS cc_start: 0.8432 (mttm) cc_final: 0.8161 (mttt) REVERT: B 159 PHE cc_start: 0.8522 (m-80) cc_final: 0.8276 (m-80) REVERT: B 186 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8360 (t) REVERT: B 359 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7193 (mt-10) REVERT: B 389 PRO cc_start: 0.8321 (Cg_endo) cc_final: 0.8096 (Cg_exo) REVERT: E 8 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7745 (mp) REVERT: E 20 ARG cc_start: 0.7134 (mtp85) cc_final: 0.6553 (ttm-80) REVERT: E 33 GLU cc_start: 0.7800 (tt0) cc_final: 0.7345 (tt0) REVERT: E 41 MET cc_start: 0.8281 (mmt) cc_final: 0.7710 (mmm) REVERT: E 78 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7554 (mt-10) REVERT: E 81 ARG cc_start: 0.7183 (ttm110) cc_final: 0.6784 (mtm110) REVERT: E 186 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8337 (t) REVERT: E 318 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.5775 (tpt170) REVERT: E 365 GLN cc_start: 0.6896 (tp40) cc_final: 0.6651 (tm-30) REVERT: E 410 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7420 (ttm170) REVERT: E 414 GLN cc_start: 0.7973 (mt0) cc_final: 0.7662 (tt0) REVERT: E 523 ARG cc_start: 0.7476 (ptt-90) cc_final: 0.6970 (ptt180) REVERT: G 13 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7295 (pm20) REVERT: G 33 GLU cc_start: 0.7501 (tt0) cc_final: 0.7193 (tm-30) REVERT: G 73 LYS cc_start: 0.8404 (mttm) cc_final: 0.8132 (mttt) REVERT: G 159 PHE cc_start: 0.8545 (m-80) cc_final: 0.8319 (m-80) REVERT: G 186 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8317 (t) REVERT: G 199 ASP cc_start: 0.8256 (m-30) cc_final: 0.8021 (m-30) REVERT: G 365 GLN cc_start: 0.7071 (OUTLIER) cc_final: 0.6841 (mm-40) REVERT: G 610 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7240 (mt-10) REVERT: I 20 ARG cc_start: 0.7320 (mtp-110) cc_final: 0.6965 (mmm160) REVERT: I 37 GLU cc_start: 0.7137 (tt0) cc_final: 0.6787 (mt-10) REVERT: I 329 GLN cc_start: 0.5983 (mm-40) cc_final: 0.5759 (mm110) REVERT: I 348 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7386 (tm-30) REVERT: I 385 PRO cc_start: 0.7705 (Cg_endo) cc_final: 0.7483 (Cg_exo) REVERT: K 33 GLU cc_start: 0.7814 (tt0) cc_final: 0.7420 (tt0) REVERT: K 41 MET cc_start: 0.8285 (mmt) cc_final: 0.7707 (mmm) REVERT: K 81 ARG cc_start: 0.7188 (ttm110) cc_final: 0.6808 (mtm110) REVERT: K 186 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8354 (t) REVERT: K 318 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.5933 (tpt170) REVERT: K 458 LYS cc_start: 0.8105 (tmtp) cc_final: 0.7875 (tttt) REVERT: K 574 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7872 (pt0) REVERT: K 610 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7491 (mm-30) outliers start: 60 outliers final: 23 residues processed: 415 average time/residue: 1.9242 time to fit residues: 910.6804 Evaluate side-chains 414 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 376 time to evaluate : 3.565 ------------------------------------------------------------------------------- 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 37 GLU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 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 3 GLN Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 186 THR 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 13 GLN Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 365 GLN Chi-restraints excluded: chain G residue 523 ARG Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 348 GLU Chi-restraints excluded: chain I residue 576 ILE Chi-restraints excluded: chain I residue 640 SER Chi-restraints excluded: chain 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 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: 3.9990 chunk 309 optimal weight: 20.0000 chunk 179 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 chunk 347 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 398 optimal weight: 8.9990 chunk 219 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 186 optimal weight: 0.8980 chunk 160 optimal weight: 20.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 13 GLN B 309 ASN E 309 ASN E 339 ASN G 13 GLN G 309 ASN I 191 GLN I 409 GLN K 3 GLN K 46 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 = 0.3618 r_free = 0.3618 target = 0.137145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.100785 restraints weight = 54340.107| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.70 r_work: 0.2986 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1433 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= 0.127 Angle : 0.572 10.124 42516 Z= 0.296 Chirality : 0.043 0.164 4842 Planarity : 0.004 0.047 5580 Dihedral : 4.799 37.618 4354 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.76 % Allowed : 11.45 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.63 (0.13), residues: 4062 helix: 1.32 (0.13), residues: 1434 sheet: 0.60 (0.19), residues: 786 loop : -0.32 (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 A 607 ARG 0.007 0.000 ARG B 81 Details of bonding type rmsd hydrogen bonds : bond 0.04402 ( 1198) hydrogen bonds : angle 4.73029 ( 3312) covalent geometry : bond 0.00284 (31320) covalent geometry : angle 0.57235 (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 429 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 377 time to evaluate : 3.265 Fit side-chains REVERT: A 33 GLU cc_start: 0.7687 (pp20) cc_final: 0.7381 (pp20) REVERT: A 34 VAL cc_start: 0.8110 (t) cc_final: 0.7667 (p) REVERT: A 348 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7402 (tm-30) REVERT: A 410 ARG cc_start: 0.7638 (ttm-80) cc_final: 0.7428 (ttm-80) REVERT: B 3 GLN cc_start: 0.7071 (mt0) cc_final: 0.6540 (mt0) REVERT: B 13 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7999 (pt0) REVERT: B 73 LYS cc_start: 0.8432 (mttm) cc_final: 0.8178 (mttt) REVERT: B 186 THR cc_start: 0.8550 (OUTLIER) cc_final: 0.8305 (t) REVERT: B 359 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7271 (mt-10) REVERT: B 389 PRO cc_start: 0.8319 (Cg_endo) cc_final: 0.8118 (Cg_exo) REVERT: B 410 ARG cc_start: 0.7426 (ttm-80) cc_final: 0.6935 (ttp-110) REVERT: B 610 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7194 (mt-10) REVERT: E 8 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7746 (mp) REVERT: E 20 ARG cc_start: 0.7151 (mtp85) cc_final: 0.6569 (ttm-80) REVERT: E 33 GLU cc_start: 0.7884 (tt0) cc_final: 0.7414 (tm-30) REVERT: E 41 MET cc_start: 0.8281 (mmt) cc_final: 0.7718 (mmm) REVERT: E 78 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7580 (mt-10) REVERT: E 81 ARG cc_start: 0.7189 (ttm110) cc_final: 0.6816 (mtm110) REVERT: E 318 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.5786 (tpt170) REVERT: E 365 GLN cc_start: 0.6822 (tp40) cc_final: 0.6586 (tm-30) REVERT: E 414 GLN cc_start: 0.8021 (mt0) cc_final: 0.7712 (tt0) REVERT: E 523 ARG cc_start: 0.7449 (ptt-90) cc_final: 0.6945 (ptt180) REVERT: E 574 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7878 (pt0) REVERT: G 33 GLU cc_start: 0.7484 (tt0) cc_final: 0.7274 (tt0) REVERT: G 73 LYS cc_start: 0.8386 (mttm) cc_final: 0.8126 (mttt) REVERT: G 186 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8306 (t) REVERT: G 199 ASP cc_start: 0.8287 (m-30) cc_final: 0.8045 (m-30) REVERT: G 610 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6990 (mt-10) REVERT: I 20 ARG cc_start: 0.7416 (mtp-110) cc_final: 0.7087 (mmm160) REVERT: I 37 GLU cc_start: 0.7155 (tt0) cc_final: 0.6826 (mt-10) REVERT: I 329 GLN cc_start: 0.6024 (mm-40) cc_final: 0.5774 (mm110) REVERT: I 348 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7424 (tm-30) REVERT: I 385 PRO cc_start: 0.7688 (Cg_endo) cc_final: 0.7479 (Cg_exo) REVERT: K 33 GLU cc_start: 0.7809 (tt0) cc_final: 0.7423 (tm-30) REVERT: K 41 MET cc_start: 0.8342 (mmt) cc_final: 0.7758 (mmm) REVERT: K 78 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7512 (mt-10) REVERT: K 81 ARG cc_start: 0.7190 (ttm110) cc_final: 0.6821 (mtm110) REVERT: K 186 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8355 (t) REVERT: K 318 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.5751 (tpt170) REVERT: K 458 LYS cc_start: 0.8088 (tmtp) cc_final: 0.7872 (tttt) REVERT: K 574 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7847 (pt0) REVERT: K 610 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7534 (mm-30) outliers start: 52 outliers final: 21 residues processed: 404 average time/residue: 1.8666 time to fit residues: 856.4921 Evaluate side-chains 405 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 371 time to evaluate : 3.339 ------------------------------------------------------------------------------- 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 13 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 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 227 VAL Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 518 LYS Chi-restraints excluded: chain G residue 523 ARG Chi-restraints excluded: chain G residue 611 SER Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 348 GLU Chi-restraints excluded: chain I residue 576 ILE Chi-restraints excluded: chain I residue 640 SER Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 318 ARG Chi-restraints excluded: chain K residue 540 LEU Chi-restraints excluded: chain K residue 574 GLU Chi-restraints excluded: chain K residue 610 GLU Chi-restraints excluded: chain K residue 640 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 271 optimal weight: 20.0000 chunk 391 optimal weight: 7.9990 chunk 267 optimal weight: 0.9990 chunk 252 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 314 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 chunk 250 optimal weight: 10.0000 chunk 221 optimal weight: 0.0070 chunk 154 optimal weight: 0.0170 chunk 347 optimal weight: 6.9990 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 659 HIS ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN B 309 ASN E 309 ASN E 339 ASN E 659 HIS G 13 GLN G 309 ASN I 191 GLN ** I 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN K 46 GLN K 309 ASN K 659 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.141029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.107934 restraints weight = 57155.749| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.98 r_work: 0.3064 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 31320 Z= 0.092 Angle : 0.507 9.723 42516 Z= 0.261 Chirality : 0.041 0.159 4842 Planarity : 0.004 0.047 5580 Dihedral : 4.255 34.933 4354 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.97 % Allowed : 12.26 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.98 (0.13), residues: 4062 helix: 1.69 (0.14), residues: 1428 sheet: 0.70 (0.19), residues: 780 loop : -0.12 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 12 HIS 0.006 0.001 HIS I 463 PHE 0.025 0.001 PHE E 595 TYR 0.019 0.001 TYR A 607 ARG 0.008 0.000 ARG B 81 Details of bonding type rmsd hydrogen bonds : bond 0.03263 ( 1198) hydrogen bonds : angle 4.42520 ( 3312) covalent geometry : bond 0.00199 (31320) covalent geometry : angle 0.50725 (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 419 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 392 time to evaluate : 3.325 Fit side-chains REVERT: A 8 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7711 (pp) REVERT: A 20 ARG cc_start: 0.7234 (mtp85) cc_final: 0.6944 (mmm160) REVERT: A 34 VAL cc_start: 0.8086 (t) cc_final: 0.7781 (p) REVERT: A 81 ARG cc_start: 0.7319 (mtm110) cc_final: 0.6943 (ptp-170) REVERT: A 318 ARG cc_start: 0.7193 (ttm110) cc_final: 0.6941 (tpp80) REVERT: A 410 ARG cc_start: 0.7609 (ttm-80) cc_final: 0.7399 (ttm-80) REVERT: B 3 GLN cc_start: 0.7097 (mt0) cc_final: 0.6629 (mt0) REVERT: B 186 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.8039 (t) REVERT: B 610 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6784 (mt-10) REVERT: E 20 ARG cc_start: 0.7063 (mtp85) cc_final: 0.6477 (ttm-80) REVERT: E 33 GLU cc_start: 0.7747 (tt0) cc_final: 0.7278 (tm-30) REVERT: E 78 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7514 (mt-10) REVERT: E 81 ARG cc_start: 0.7209 (ttm110) cc_final: 0.6957 (mtm110) REVERT: E 309 ASN cc_start: 0.7730 (m-40) cc_final: 0.7126 (m-40) REVERT: E 365 GLN cc_start: 0.6948 (tp40) cc_final: 0.6695 (tm-30) REVERT: E 410 ARG cc_start: 0.7801 (ttm170) cc_final: 0.7170 (ttm110) REVERT: E 414 GLN cc_start: 0.7992 (mt0) cc_final: 0.7662 (tt0) REVERT: E 610 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7469 (mt-10) REVERT: E 642 GLU cc_start: 0.5373 (pm20) cc_final: 0.5119 (pp20) REVERT: G 3 GLN cc_start: 0.6955 (mt0) cc_final: 0.6643 (tt0) REVERT: G 33 GLU cc_start: 0.7669 (tt0) cc_final: 0.7201 (tt0) REVERT: G 186 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.8059 (t) REVERT: G 610 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6634 (mt-10) REVERT: I 20 ARG cc_start: 0.7460 (mtp-110) cc_final: 0.7162 (mmm160) REVERT: I 37 GLU cc_start: 0.7042 (tt0) cc_final: 0.6744 (mt-10) REVERT: I 81 ARG cc_start: 0.7293 (mtm110) cc_final: 0.6877 (ptp-170) REVERT: I 318 ARG cc_start: 0.7189 (ttm110) cc_final: 0.6935 (tpp80) REVERT: I 610 GLU cc_start: 0.7233 (mm-30) cc_final: 0.7005 (mt-10) REVERT: K 33 GLU cc_start: 0.7776 (tt0) cc_final: 0.7452 (tm-30) REVERT: K 41 MET cc_start: 0.8283 (mmt) cc_final: 0.7597 (mmm) REVERT: K 46 GLN cc_start: 0.8012 (tp-100) cc_final: 0.7804 (tp40) REVERT: K 78 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7408 (mt-10) REVERT: K 81 ARG cc_start: 0.7215 (ttm110) cc_final: 0.6905 (mtm110) REVERT: K 186 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8217 (t) REVERT: K 309 ASN cc_start: 0.7686 (m-40) cc_final: 0.7073 (m-40) REVERT: K 410 ARG cc_start: 0.7828 (ttm170) cc_final: 0.7182 (ttm110) REVERT: K 458 LYS cc_start: 0.8211 (tmtp) cc_final: 0.7933 (tttt) REVERT: K 523 ARG cc_start: 0.7398 (mtm180) cc_final: 0.7051 (ptt-90) outliers start: 27 outliers final: 7 residues processed: 400 average time/residue: 1.7913 time to fit residues: 821.9954 Evaluate side-chains 379 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 368 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 518 LYS Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain I residue 547 MET Chi-restraints excluded: chain I residue 576 ILE Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 540 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 185 optimal weight: 10.0000 chunk 233 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 335 optimal weight: 20.0000 chunk 161 optimal weight: 0.0070 chunk 184 optimal weight: 6.9990 chunk 374 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 225 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 overall best weight: 4.8006 ------------------------------------------------------------------------------- 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 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN B 309 ASN E 339 ASN E 492 HIS ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 309 ASN I 409 GLN K 492 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.135419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.099905 restraints weight = 59957.920| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.01 r_work: 0.2962 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1349 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= 0.214 Angle : 0.680 10.517 42516 Z= 0.353 Chirality : 0.048 0.186 4842 Planarity : 0.005 0.068 5580 Dihedral : 5.097 37.980 4354 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.16 % Allowed : 12.61 % Favored : 86.23 % 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: 0.60 (0.13), residues: 4062 helix: 1.23 (0.13), residues: 1428 sheet: 0.63 (0.19), residues: 786 loop : -0.29 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 97 HIS 0.005 0.002 HIS G 583 PHE 0.026 0.002 PHE A 595 TYR 0.020 0.003 TYR B 493 ARG 0.005 0.001 ARG K 627 Details of bonding type rmsd hydrogen bonds : bond 0.05642 ( 1198) hydrogen bonds : angle 4.92561 ( 3312) covalent geometry : bond 0.00497 (31320) covalent geometry : angle 0.67994 (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 415 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 382 time to evaluate : 3.396 Fit side-chains REVERT: A 33 GLU cc_start: 0.7713 (pp20) cc_final: 0.7469 (pp20) REVERT: A 329 GLN cc_start: 0.5976 (mt0) cc_final: 0.5245 (mm-40) REVERT: A 410 ARG cc_start: 0.7680 (ttm-80) cc_final: 0.7461 (ttm-80) REVERT: B 159 PHE cc_start: 0.8540 (m-80) cc_final: 0.8293 (m-80) REVERT: B 186 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8318 (t) REVERT: B 610 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7237 (mt-10) REVERT: E 20 ARG cc_start: 0.7287 (mtp85) cc_final: 0.6706 (ttm-80) REVERT: E 33 GLU cc_start: 0.7765 (tt0) cc_final: 0.7395 (tt0) REVERT: E 81 ARG cc_start: 0.7203 (ttm110) cc_final: 0.6918 (mtm110) REVERT: E 318 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.5748 (tpt170) REVERT: E 365 GLN cc_start: 0.6868 (tp40) cc_final: 0.6602 (tm-30) REVERT: E 414 GLN cc_start: 0.8032 (mt0) cc_final: 0.7720 (tt0) REVERT: E 547 MET cc_start: 0.9071 (mmp) cc_final: 0.8650 (mmp) REVERT: E 642 GLU cc_start: 0.5263 (pm20) cc_final: 0.4967 (pp20) REVERT: G 33 GLU cc_start: 0.7663 (tt0) cc_final: 0.7305 (tt0) REVERT: G 186 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8324 (t) REVERT: G 199 ASP cc_start: 0.8251 (m-30) cc_final: 0.8024 (m-30) REVERT: G 610 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7165 (mt-10) REVERT: I 20 ARG cc_start: 0.7559 (mtp-110) cc_final: 0.7225 (mmm160) REVERT: I 37 GLU cc_start: 0.7222 (tt0) cc_final: 0.6757 (mt-10) REVERT: I 329 GLN cc_start: 0.6041 (mt0) cc_final: 0.5281 (mm-40) REVERT: I 521 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7819 (mt-10) REVERT: K 33 GLU cc_start: 0.7836 (tt0) cc_final: 0.7461 (tt0) REVERT: K 41 MET cc_start: 0.8358 (mmt) cc_final: 0.7771 (mmm) REVERT: K 81 ARG cc_start: 0.7188 (ttm110) cc_final: 0.6902 (mtm110) REVERT: K 458 LYS cc_start: 0.8100 (tmtp) cc_final: 0.7868 (tttt) REVERT: K 547 MET cc_start: 0.9067 (mmp) cc_final: 0.8651 (mmp) outliers start: 33 outliers final: 17 residues processed: 402 average time/residue: 1.8398 time to fit residues: 840.6237 Evaluate side-chains 389 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 368 time to evaluate : 3.122 ------------------------------------------------------------------------------- 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 B residue 37 GLU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 518 LYS Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 256 GLU Chi-restraints excluded: chain I residue 521 GLU Chi-restraints excluded: chain I residue 576 ILE Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 540 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 373 optimal weight: 1.9990 chunk 271 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 372 optimal weight: 9.9990 chunk 230 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 376 optimal weight: 0.5980 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN B 309 ASN E 309 ASN E 339 ASN G 13 GLN G 46 GLN G 309 ASN I 191 GLN I 409 GLN K 46 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 = 0.3608 r_free = 0.3608 target = 0.136312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.101179 restraints weight = 57765.209| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.96 r_work: 0.2979 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- 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 = 0.46 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: 0.8484 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 31320 Z= 0.166 Angle : 0.626 10.948 42516 Z= 0.325 Chirality : 0.045 0.177 4842 Planarity : 0.005 0.056 5580 Dihedral : 4.982 37.635 4354 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.91 % Allowed : 13.08 % Favored : 86.01 % 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: 0.60 (0.13), residues: 4062 helix: 1.23 (0.13), residues: 1428 sheet: 0.64 (0.19), residues: 786 loop : -0.29 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 97 HIS 0.004 0.001 HIS I 463 PHE 0.026 0.002 PHE E 595 TYR 0.020 0.002 TYR K 607 ARG 0.006 0.001 ARG G 436 Details of bonding type rmsd hydrogen bonds : bond 0.05014 ( 1198) hydrogen bonds : angle 4.82535 ( 3312) covalent geometry : bond 0.00379 (31320) covalent geometry : angle 0.62599 (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 395 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 370 time to evaluate : 3.439 Fit side-chains REVERT: A 33 GLU cc_start: 0.7710 (pp20) cc_final: 0.7476 (pp20) REVERT: A 329 GLN cc_start: 0.6005 (mt0) cc_final: 0.5281 (mm-40) REVERT: A 410 ARG cc_start: 0.7634 (ttm-80) cc_final: 0.7417 (ttm-80) REVERT: A 610 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7231 (mt-10) REVERT: B 186 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8331 (t) REVERT: B 610 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7147 (mt-10) REVERT: E 20 ARG cc_start: 0.7282 (mtp85) cc_final: 0.6706 (ttm-80) REVERT: E 33 GLU cc_start: 0.7778 (tt0) cc_final: 0.7438 (tt0) REVERT: E 41 MET cc_start: 0.8236 (mmt) cc_final: 0.7664 (mmm) REVERT: E 78 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7467 (mt-10) REVERT: E 81 ARG cc_start: 0.7158 (ttm110) cc_final: 0.6818 (mtm110) REVERT: E 365 GLN cc_start: 0.6824 (tp40) cc_final: 0.6581 (tm-30) REVERT: E 414 GLN cc_start: 0.7997 (mt0) cc_final: 0.7679 (tt0) REVERT: E 642 GLU cc_start: 0.5121 (pm20) cc_final: 0.4848 (pp20) REVERT: G 33 GLU cc_start: 0.7627 (tt0) cc_final: 0.7219 (tt0) REVERT: G 186 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8337 (t) REVERT: G 199 ASP cc_start: 0.8226 (m-30) cc_final: 0.7985 (m-30) REVERT: G 610 GLU cc_start: 0.7267 (mm-30) cc_final: 0.7056 (mt-10) REVERT: I 20 ARG cc_start: 0.7423 (mtp-110) cc_final: 0.7055 (mmm160) REVERT: I 37 GLU cc_start: 0.7196 (tt0) cc_final: 0.6720 (mt-10) REVERT: I 205 GLU cc_start: 0.8228 (tt0) cc_final: 0.8009 (mm-30) REVERT: I 329 GLN cc_start: 0.6047 (mt0) cc_final: 0.5289 (mm-40) REVERT: I 521 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7749 (mt-10) REVERT: I 610 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7155 (mt-10) REVERT: K 33 GLU cc_start: 0.7851 (tt0) cc_final: 0.7504 (tt0) REVERT: K 41 MET cc_start: 0.8322 (mmt) cc_final: 0.7748 (mmm) REVERT: K 81 ARG cc_start: 0.7188 (ttm110) cc_final: 0.6845 (mtm110) REVERT: K 458 LYS cc_start: 0.8108 (tmtp) cc_final: 0.7875 (tttt) REVERT: K 523 ARG cc_start: 0.7464 (mtm180) cc_final: 0.7062 (ptt-90) REVERT: K 547 MET cc_start: 0.9061 (mmp) cc_final: 0.8630 (mmp) outliers start: 25 outliers final: 15 residues processed: 387 average time/residue: 1.8825 time to fit residues: 828.9214 Evaluate side-chains 383 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 365 time to evaluate : 3.140 ------------------------------------------------------------------------------- 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 B residue 37 GLU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 518 LYS Chi-restraints excluded: chain E residue 3 GLN 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 193 MET Chi-restraints excluded: chain G residue 256 GLU Chi-restraints excluded: chain I residue 521 GLU Chi-restraints excluded: chain I residue 576 ILE Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 540 LEU 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: 0.4980 chunk 72 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 334 optimal weight: 8.9990 chunk 85 optimal weight: 0.0980 chunk 53 optimal weight: 1.9990 chunk 370 optimal weight: 4.9990 chunk 348 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 326 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN B 309 ASN E 309 ASN E 339 ASN G 13 GLN G 46 GLN G 309 ASN I 409 GLN K 46 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 = 0.3645 r_free = 0.3645 target = 0.139192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.104340 restraints weight = 66611.173| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.33 r_work: 0.3022 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 31320 Z= 0.100 Angle : 0.530 10.243 42516 Z= 0.273 Chirality : 0.042 0.160 4842 Planarity : 0.004 0.049 5580 Dihedral : 4.467 34.700 4354 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.63 % Allowed : 13.33 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.97 (0.13), residues: 4062 helix: 1.61 (0.14), residues: 1422 sheet: 0.69 (0.19), residues: 810 loop : -0.08 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 97 HIS 0.006 0.001 HIS I 463 PHE 0.026 0.001 PHE E 595 TYR 0.019 0.002 TYR K 607 ARG 0.006 0.000 ARG I 410 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 1198) hydrogen bonds : angle 4.53030 ( 3312) covalent geometry : bond 0.00219 (31320) covalent geometry : angle 0.52997 (42516) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33181.27 seconds wall clock time: 569 minutes 40.52 seconds (34180.52 seconds total)