Starting phenix.real_space_refine on Sun Aug 24 18:09:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j4t_35977/08_2025/8j4t_35977.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j4t_35977/08_2025/8j4t_35977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j4t_35977/08_2025/8j4t_35977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j4t_35977/08_2025/8j4t_35977.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j4t_35977/08_2025/8j4t_35977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j4t_35977/08_2025/8j4t_35977.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.004 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 64 5.16 5 C 14564 2.51 5 N 3708 2.21 5 O 4292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22628 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3850 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 461} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1807 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain: "C" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3850 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 461} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1807 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain: "D" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3850 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 461} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3850 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 461} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1807 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain: "H" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1807 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 5, 'TRANS': 217} Time building chain proxies: 4.74, per 1000 atoms: 0.21 Number of scatterers: 22628 At special positions: 0 Unit cell: (165, 187, 113, 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 64 16.00 O 4292 8.00 N 3708 7.00 C 14564 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: 1.89 Conformation dependent library (CDL) restraints added in 993.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5224 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 20 sheets defined 50.3% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 31 through 47 Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 60 through 64 removed outlier: 3.552A pdb=" N HIS A 63 " --> pdb=" O TYR A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 93 removed outlier: 3.895A pdb=" N VAL A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 147 Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.898A pdb=" N ASN A 271 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.611A pdb=" N TYR A 326 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 371 removed outlier: 4.155A pdb=" N SER A 368 " --> pdb=" O LYS A 364 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 395 Processing helix chain 'A' and resid 396 through 399 removed outlier: 4.333A pdb=" N GLU A 399 " --> pdb=" O PRO A 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 396 through 399' Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 447 through 457 removed outlier: 4.077A pdb=" N CYS A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 457 " --> pdb=" O CYS A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 493 Processing helix chain 'A' and resid 493 through 503 Processing helix chain 'A' and resid 511 through 520 Processing helix chain 'A' and resid 521 through 529 Processing helix chain 'A' and resid 532 through 540 removed outlier: 3.703A pdb=" N SER A 540 " --> pdb=" O TYR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 551 Processing helix chain 'A' and resid 553 through 563 Processing helix chain 'A' and resid 566 through 574 removed outlier: 3.925A pdb=" N LYS A 570 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 9 Processing helix chain 'G' and resid 22 through 38 removed outlier: 3.698A pdb=" N ILE G 26 " --> pdb=" O GLY G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 61 Processing helix chain 'G' and resid 72 through 81 Processing helix chain 'G' and resid 81 through 91 removed outlier: 3.878A pdb=" N PHE G 85 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LYS G 87 " --> pdb=" O ARG G 83 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASP G 88 " --> pdb=" O PRO G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 121 removed outlier: 3.538A pdb=" N ASN G 121 " --> pdb=" O LEU G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 144 removed outlier: 3.790A pdb=" N GLN G 136 " --> pdb=" O ASN G 132 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS G 144 " --> pdb=" O ASP G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 155 removed outlier: 3.501A pdb=" N ARG G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 167 Processing helix chain 'G' and resid 168 through 181 Processing helix chain 'G' and resid 204 through 213 Processing helix chain 'C' and resid 31 through 47 Processing helix chain 'C' and resid 47 through 52 Processing helix chain 'C' and resid 60 through 64 removed outlier: 3.553A pdb=" N HIS C 63 " --> pdb=" O TYR C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 93 removed outlier: 3.895A pdb=" N VAL C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 93 " --> pdb=" O LEU C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 147 Processing helix chain 'C' and resid 264 through 278 removed outlier: 3.899A pdb=" N ASN C 271 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N TYR C 272 " --> pdb=" O SER C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 308 Processing helix chain 'C' and resid 321 through 326 removed outlier: 3.611A pdb=" N TYR C 326 " --> pdb=" O GLU C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 removed outlier: 4.156A pdb=" N SER C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C 369 " --> pdb=" O ALA C 365 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 395 Processing helix chain 'C' and resid 396 through 399 removed outlier: 4.332A pdb=" N GLU C 399 " --> pdb=" O PRO C 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 396 through 399' Processing helix chain 'C' and resid 413 through 423 Processing helix chain 'C' and resid 447 through 457 removed outlier: 4.076A pdb=" N CYS C 453 " --> pdb=" O GLY C 449 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 457 " --> pdb=" O CYS C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 493 Processing helix chain 'C' and resid 493 through 503 Processing helix chain 'C' and resid 511 through 520 Processing helix chain 'C' and resid 521 through 529 Processing helix chain 'C' and resid 532 through 540 removed outlier: 3.703A pdb=" N SER C 540 " --> pdb=" O TYR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 551 Processing helix chain 'C' and resid 553 through 563 Processing helix chain 'C' and resid 566 through 574 removed outlier: 3.926A pdb=" N LYS C 570 " --> pdb=" O PHE C 566 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 9 Processing helix chain 'F' and resid 22 through 38 removed outlier: 3.698A pdb=" N ILE F 26 " --> pdb=" O GLY F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 61 Processing helix chain 'F' and resid 72 through 81 Processing helix chain 'F' and resid 81 through 91 removed outlier: 3.878A pdb=" N PHE F 85 " --> pdb=" O ILE F 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LYS F 87 " --> pdb=" O ARG F 83 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASP F 88 " --> pdb=" O PRO F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 121 removed outlier: 3.538A pdb=" N ASN F 121 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 144 removed outlier: 3.790A pdb=" N GLN F 136 " --> pdb=" O ASN F 132 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS F 144 " --> pdb=" O ASP F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 removed outlier: 3.501A pdb=" N ARG F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 167 Processing helix chain 'F' and resid 168 through 181 Processing helix chain 'F' and resid 204 through 213 Processing helix chain 'D' and resid 31 through 47 Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 60 through 64 removed outlier: 3.552A pdb=" N HIS D 63 " --> pdb=" O TYR D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 93 removed outlier: 3.894A pdb=" N VAL D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 147 Processing helix chain 'D' and resid 264 through 278 removed outlier: 3.898A pdb=" N ASN D 271 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR D 272 " --> pdb=" O SER D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 308 Processing helix chain 'D' and resid 321 through 326 removed outlier: 3.611A pdb=" N TYR D 326 " --> pdb=" O GLU D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 371 removed outlier: 4.155A pdb=" N SER D 368 " --> pdb=" O LYS D 364 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA D 369 " --> pdb=" O ALA D 365 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE D 371 " --> pdb=" O SER D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 395 Processing helix chain 'D' and resid 396 through 399 removed outlier: 4.331A pdb=" N GLU D 399 " --> pdb=" O PRO D 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 396 through 399' Processing helix chain 'D' and resid 413 through 423 Processing helix chain 'D' and resid 447 through 457 removed outlier: 4.077A pdb=" N CYS D 453 " --> pdb=" O GLY D 449 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 457 " --> pdb=" O CYS D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 493 Processing helix chain 'D' and resid 493 through 503 Processing helix chain 'D' and resid 511 through 520 Processing helix chain 'D' and resid 521 through 529 Processing helix chain 'D' and resid 532 through 540 removed outlier: 3.703A pdb=" N SER D 540 " --> pdb=" O TYR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 551 Processing helix chain 'D' and resid 553 through 563 Processing helix chain 'D' and resid 566 through 574 removed outlier: 3.925A pdb=" N LYS D 570 " --> pdb=" O PHE D 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 47 Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 60 through 64 removed outlier: 3.552A pdb=" N HIS B 63 " --> pdb=" O TYR B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.895A pdb=" N VAL B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 147 Processing helix chain 'B' and resid 264 through 278 removed outlier: 3.899A pdb=" N ASN B 271 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 308 Processing helix chain 'B' and resid 321 through 326 removed outlier: 3.612A pdb=" N TYR B 326 " --> pdb=" O GLU B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 371 removed outlier: 4.155A pdb=" N SER B 368 " --> pdb=" O LYS B 364 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 369 " --> pdb=" O ALA B 365 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE B 371 " --> pdb=" O SER B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 395 Processing helix chain 'B' and resid 396 through 399 removed outlier: 4.332A pdb=" N GLU B 399 " --> pdb=" O PRO B 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 396 through 399' Processing helix chain 'B' and resid 413 through 423 Processing helix chain 'B' and resid 447 through 457 removed outlier: 4.077A pdb=" N CYS B 453 " --> pdb=" O GLY B 449 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 457 " --> pdb=" O CYS B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 493 Processing helix chain 'B' and resid 493 through 503 Processing helix chain 'B' and resid 511 through 520 Processing helix chain 'B' and resid 521 through 529 Processing helix chain 'B' and resid 532 through 540 removed outlier: 3.703A pdb=" N SER B 540 " --> pdb=" O TYR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 551 Processing helix chain 'B' and resid 553 through 563 Processing helix chain 'B' and resid 566 through 574 removed outlier: 3.925A pdb=" N LYS B 570 " --> pdb=" O PHE B 566 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 22 through 38 removed outlier: 3.698A pdb=" N ILE E 26 " --> pdb=" O GLY E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 61 Processing helix chain 'E' and resid 72 through 81 Processing helix chain 'E' and resid 81 through 91 removed outlier: 3.877A pdb=" N PHE E 85 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LYS E 87 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ASP E 88 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 121 removed outlier: 3.538A pdb=" N ASN E 121 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 144 removed outlier: 3.790A pdb=" N GLN E 136 " --> pdb=" O ASN E 132 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 155 removed outlier: 3.501A pdb=" N ARG E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 167 Processing helix chain 'E' and resid 168 through 181 Processing helix chain 'E' and resid 204 through 213 Processing helix chain 'H' and resid 2 through 9 Processing helix chain 'H' and resid 22 through 38 removed outlier: 3.699A pdb=" N ILE H 26 " --> pdb=" O GLY H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 61 Processing helix chain 'H' and resid 72 through 81 Processing helix chain 'H' and resid 81 through 91 removed outlier: 3.878A pdb=" N PHE H 85 " --> pdb=" O ILE H 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LYS H 87 " --> pdb=" O ARG H 83 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASP H 88 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 121 removed outlier: 3.538A pdb=" N ASN H 121 " --> pdb=" O LEU H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 144 removed outlier: 3.790A pdb=" N GLN H 136 " --> pdb=" O ASN H 132 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS H 144 " --> pdb=" O ASP H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 155 removed outlier: 3.501A pdb=" N ARG H 149 " --> pdb=" O SER H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 167 Processing helix chain 'H' and resid 168 through 181 Processing helix chain 'H' and resid 204 through 213 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 20 removed outlier: 5.480A pdb=" N PHE A 3 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ASP A 76 " --> pdb=" O PHE A 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 20 removed outlier: 5.480A pdb=" N PHE A 3 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ASP A 76 " --> pdb=" O PHE A 3 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 149 through 154 removed outlier: 6.582A pdb=" N LYS A 150 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU A 286 " --> pdb=" O LYS A 150 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE A 152 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLU A 288 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE A 154 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N PHE A 316 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TYR A 285 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N SER A 318 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE A 287 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL A 26 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL A 336 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N PHE A 28 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 405 through 407 removed outlier: 5.894A pdb=" N VAL A 375 " --> pdb=" O ILE A 428 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LYS A 430 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N LEU A 377 " --> pdb=" O LYS A 430 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N TYR A 506 " --> pdb=" O HIS A 427 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE A 429 " --> pdb=" O TYR A 506 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 69 through 71 removed outlier: 3.624A pdb=" N GLY G 71 " --> pdb=" O ALA G 46 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N SER G 43 " --> pdb=" O LYS G 158 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N PHE G 160 " --> pdb=" O SER G 43 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ALA G 45 " --> pdb=" O PHE G 160 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE G 13 " --> pdb=" O ILE G 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 16 through 20 removed outlier: 5.480A pdb=" N PHE C 3 " --> pdb=" O ASP C 76 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ASP C 76 " --> pdb=" O PHE C 3 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 16 through 20 removed outlier: 5.480A pdb=" N PHE C 3 " --> pdb=" O ASP C 76 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ASP C 76 " --> pdb=" O PHE C 3 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 149 through 154 removed outlier: 6.582A pdb=" N LYS C 150 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU C 286 " --> pdb=" O LYS C 150 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE C 152 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLU C 288 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE C 154 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N PHE C 316 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TYR C 285 " --> pdb=" O PHE C 316 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N SER C 318 " --> pdb=" O TYR C 285 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE C 287 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL C 26 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL C 336 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N PHE C 28 " --> pdb=" O VAL C 336 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 405 through 407 removed outlier: 5.894A pdb=" N VAL C 375 " --> pdb=" O ILE C 428 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LYS C 430 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N LEU C 377 " --> pdb=" O LYS C 430 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N TYR C 506 " --> pdb=" O HIS C 427 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE C 429 " --> pdb=" O TYR C 506 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 69 through 71 removed outlier: 3.623A pdb=" N GLY F 71 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N SER F 43 " --> pdb=" O LYS F 158 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N PHE F 160 " --> pdb=" O SER F 43 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ALA F 45 " --> pdb=" O PHE F 160 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE F 13 " --> pdb=" O ILE F 188 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 16 through 20 removed outlier: 5.479A pdb=" N PHE D 3 " --> pdb=" O ASP D 76 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ASP D 76 " --> pdb=" O PHE D 3 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 16 through 20 removed outlier: 5.479A pdb=" N PHE D 3 " --> pdb=" O ASP D 76 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ASP D 76 " --> pdb=" O PHE D 3 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 149 through 154 removed outlier: 6.581A pdb=" N LYS D 150 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU D 286 " --> pdb=" O LYS D 150 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE D 152 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLU D 288 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE D 154 " --> pdb=" O GLU D 288 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N PHE D 316 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR D 285 " --> pdb=" O PHE D 316 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N SER D 318 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE D 287 " --> pdb=" O SER D 318 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL D 26 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL D 336 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE D 28 " --> pdb=" O VAL D 336 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 405 through 407 removed outlier: 5.893A pdb=" N VAL D 375 " --> pdb=" O ILE D 428 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LYS D 430 " --> pdb=" O VAL D 375 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N LEU D 377 " --> pdb=" O LYS D 430 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N TYR D 506 " --> pdb=" O HIS D 427 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE D 429 " --> pdb=" O TYR D 506 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 16 through 20 removed outlier: 5.480A pdb=" N PHE B 3 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ASP B 76 " --> pdb=" O PHE B 3 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 16 through 20 removed outlier: 5.480A pdb=" N PHE B 3 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ASP B 76 " --> pdb=" O PHE B 3 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 149 through 154 removed outlier: 6.582A pdb=" N LYS B 150 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LEU B 286 " --> pdb=" O LYS B 150 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE B 152 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLU B 288 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE B 154 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N PHE B 316 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR B 285 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N SER B 318 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE B 287 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL B 26 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL B 336 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N PHE B 28 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 405 through 407 removed outlier: 5.894A pdb=" N VAL B 375 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LYS B 430 " --> pdb=" O VAL B 375 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N LEU B 377 " --> pdb=" O LYS B 430 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N TYR B 506 " --> pdb=" O HIS B 427 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE B 429 " --> pdb=" O TYR B 506 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 69 through 71 removed outlier: 3.623A pdb=" N GLY E 71 " --> pdb=" O ALA E 46 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N SER E 43 " --> pdb=" O LYS E 158 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N PHE E 160 " --> pdb=" O SER E 43 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ALA E 45 " --> pdb=" O PHE E 160 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE E 13 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 69 through 71 removed outlier: 3.623A pdb=" N GLY H 71 " --> pdb=" O ALA H 46 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N SER H 43 " --> pdb=" O LYS H 158 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N PHE H 160 " --> pdb=" O SER H 43 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ALA H 45 " --> pdb=" O PHE H 160 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ILE H 13 " --> pdb=" O ILE H 188 " (cutoff:3.500A) 1024 hydrogen bonds defined for protein. 2904 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: 3.98 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7240 1.35 - 1.46: 5275 1.46 - 1.58: 10433 1.58 - 1.70: 0 1.70 - 1.82: 108 Bond restraints: 23056 Sorted by residual: bond pdb=" CA GLY D 458 " pdb=" C GLY D 458 " ideal model delta sigma weight residual 1.530 1.513 0.017 1.04e-02 9.25e+03 2.78e+00 bond pdb=" CA GLY B 458 " pdb=" C GLY B 458 " ideal model delta sigma weight residual 1.530 1.513 0.017 1.04e-02 9.25e+03 2.78e+00 bond pdb=" CA GLY A 458 " pdb=" C GLY A 458 " ideal model delta sigma weight residual 1.530 1.513 0.017 1.04e-02 9.25e+03 2.70e+00 bond pdb=" CA GLY C 458 " pdb=" C GLY C 458 " ideal model delta sigma weight residual 1.530 1.514 0.017 1.04e-02 9.25e+03 2.54e+00 bond pdb=" N GLY A 458 " pdb=" CA GLY A 458 " ideal model delta sigma weight residual 1.464 1.449 0.015 1.12e-02 7.97e+03 1.90e+00 ... (remaining 23051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 30346 1.54 - 3.08: 518 3.08 - 4.63: 86 4.63 - 6.17: 30 6.17 - 7.71: 4 Bond angle restraints: 30984 Sorted by residual: angle pdb=" CA LYS C 439 " pdb=" CB LYS C 439 " pdb=" CG LYS C 439 " ideal model delta sigma weight residual 114.10 119.76 -5.66 2.00e+00 2.50e-01 8.00e+00 angle pdb=" CA LYS B 439 " pdb=" CB LYS B 439 " pdb=" CG LYS B 439 " ideal model delta sigma weight residual 114.10 119.75 -5.65 2.00e+00 2.50e-01 7.97e+00 angle pdb=" CA LYS D 439 " pdb=" CB LYS D 439 " pdb=" CG LYS D 439 " ideal model delta sigma weight residual 114.10 119.73 -5.63 2.00e+00 2.50e-01 7.92e+00 angle pdb=" CA LYS A 439 " pdb=" CB LYS A 439 " pdb=" CG LYS A 439 " ideal model delta sigma weight residual 114.10 119.72 -5.62 2.00e+00 2.50e-01 7.89e+00 angle pdb=" N GLY A 458 " pdb=" CA GLY A 458 " pdb=" C GLY A 458 " ideal model delta sigma weight residual 111.67 114.16 -2.49 9.20e-01 1.18e+00 7.34e+00 ... (remaining 30979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 12237 16.18 - 32.36: 1402 32.36 - 48.54: 265 48.54 - 64.72: 36 64.72 - 80.90: 16 Dihedral angle restraints: 13956 sinusoidal: 5816 harmonic: 8140 Sorted by residual: dihedral pdb=" CB MET C 30 " pdb=" CG MET C 30 " pdb=" SD MET C 30 " pdb=" CE MET C 30 " ideal model delta sinusoidal sigma weight residual 60.00 119.02 -59.02 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET D 30 " pdb=" CG MET D 30 " pdb=" SD MET D 30 " pdb=" CE MET D 30 " ideal model delta sinusoidal sigma weight residual 60.00 119.02 -59.02 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET B 30 " pdb=" CG MET B 30 " pdb=" SD MET B 30 " pdb=" CE MET B 30 " ideal model delta sinusoidal sigma weight residual 60.00 119.00 -59.00 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 13953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2358 0.036 - 0.073: 701 0.073 - 0.109: 242 0.109 - 0.146: 74 0.146 - 0.182: 5 Chirality restraints: 3380 Sorted by residual: chirality pdb=" CB VAL A 358 " pdb=" CA VAL A 358 " pdb=" CG1 VAL A 358 " pdb=" CG2 VAL A 358 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" CB VAL D 358 " pdb=" CA VAL D 358 " pdb=" CG1 VAL D 358 " pdb=" CG2 VAL D 358 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.29e-01 chirality pdb=" CB VAL C 358 " pdb=" CA VAL C 358 " pdb=" CG1 VAL C 358 " pdb=" CG2 VAL C 358 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.01e-01 ... (remaining 3377 not shown) Planarity restraints: 3952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A -1 " -0.040 5.00e-02 4.00e+02 6.12e-02 5.99e+00 pdb=" N PRO A 0 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 0 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 0 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B -1 " 0.040 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO B 0 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 0 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 0 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C -1 " -0.040 5.00e-02 4.00e+02 6.10e-02 5.95e+00 pdb=" N PRO C 0 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 0 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 0 " -0.034 5.00e-02 4.00e+02 ... (remaining 3949 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1013 2.73 - 3.27: 23482 3.27 - 3.82: 36514 3.82 - 4.36: 45226 4.36 - 4.90: 76183 Nonbonded interactions: 182418 Sorted by model distance: nonbonded pdb=" O LEU G 210 " pdb=" OG SER G 214 " model vdw 2.190 3.040 nonbonded pdb=" O LEU H 210 " pdb=" OG SER H 214 " model vdw 2.190 3.040 nonbonded pdb=" O LEU F 210 " pdb=" OG SER F 214 " model vdw 2.190 3.040 nonbonded pdb=" O LEU E 210 " pdb=" OG SER E 214 " model vdw 2.191 3.040 nonbonded pdb=" O TYR F 164 " pdb=" OG SER F 167 " model vdw 2.234 3.040 ... (remaining 182413 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'B' } ncs_group { reference = chain 'G' selection = chain 'F' selection = chain 'E' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.570 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 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 : 0.002 0.033 23056 Z= 0.113 Angle : 0.536 7.712 30984 Z= 0.290 Chirality : 0.042 0.182 3380 Planarity : 0.003 0.061 3952 Dihedral : 13.803 80.899 8732 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.32 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.17), residues: 2752 helix: 1.54 (0.16), residues: 1168 sheet: -1.22 (0.27), residues: 452 loop : -1.02 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 526 TYR 0.008 0.001 TYR A 312 PHE 0.024 0.001 PHE F 207 TRP 0.014 0.002 TRP D 126 HIS 0.002 0.001 HIS G 172 Details of bonding type rmsd covalent geometry : bond 0.00222 (23056) covalent geometry : angle 0.53605 (30984) hydrogen bonds : bond 0.18594 ( 976) hydrogen bonds : angle 7.32843 ( 2904) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 483 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.6691 (mmp) cc_final: 0.6490 (mmp) REVERT: A 407 GLU cc_start: 0.7466 (tt0) cc_final: 0.6933 (tt0) REVERT: G 136 GLN cc_start: 0.8098 (mt0) cc_final: 0.7446 (mp10) REVERT: C 30 MET cc_start: 0.6752 (mmp) cc_final: 0.6528 (mmp) REVERT: C 407 GLU cc_start: 0.7441 (tt0) cc_final: 0.6905 (tt0) REVERT: F 63 TYR cc_start: 0.7682 (t80) cc_final: 0.7400 (t80) REVERT: F 78 GLU cc_start: 0.7304 (tm-30) cc_final: 0.6937 (tm-30) REVERT: D 30 MET cc_start: 0.6666 (mmp) cc_final: 0.6454 (mmp) REVERT: D 407 GLU cc_start: 0.7475 (tt0) cc_final: 0.6931 (tt0) REVERT: B 30 MET cc_start: 0.6795 (mmp) cc_final: 0.6567 (mmp) REVERT: B 407 GLU cc_start: 0.7496 (tt0) cc_final: 0.6962 (tt0) REVERT: E 205 GLU cc_start: 0.6443 (pm20) cc_final: 0.5930 (mm-30) REVERT: H 149 ARG cc_start: 0.8299 (mtm180) cc_final: 0.8012 (mtm180) outliers start: 0 outliers final: 0 residues processed: 483 average time/residue: 0.1441 time to fit residues: 108.4936 Evaluate side-chains 281 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN C 538 GLN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN B 538 GLN E 150 GLN ** E 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.162733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.126488 restraints weight = 31844.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.124468 restraints weight = 26573.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.126381 restraints weight = 26427.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.126707 restraints weight = 17039.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.128373 restraints weight = 15567.231| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 23056 Z= 0.281 Angle : 0.678 7.968 30984 Z= 0.356 Chirality : 0.049 0.159 3380 Planarity : 0.004 0.048 3952 Dihedral : 4.412 18.030 3000 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.14 % Favored : 93.71 % Rotamer: Outliers : 2.12 % Allowed : 10.32 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.16), residues: 2752 helix: 1.10 (0.16), residues: 1184 sheet: -1.78 (0.25), residues: 440 loop : -1.19 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 332 TYR 0.014 0.002 TYR D 312 PHE 0.022 0.002 PHE B 28 TRP 0.010 0.002 TRP A 126 HIS 0.006 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00664 (23056) covalent geometry : angle 0.67843 (30984) hydrogen bonds : bond 0.04109 ( 976) hydrogen bonds : angle 5.57570 ( 2904) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 325 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 53 PHE cc_start: 0.8624 (m-10) cc_final: 0.8381 (m-10) REVERT: G 205 GLU cc_start: 0.7285 (pm20) cc_final: 0.6296 (mm-30) REVERT: D 53 PHE cc_start: 0.8625 (m-10) cc_final: 0.8394 (m-10) REVERT: B 53 PHE cc_start: 0.8652 (m-10) cc_final: 0.8413 (m-10) REVERT: E 149 ARG cc_start: 0.8513 (mtm180) cc_final: 0.7918 (mtm180) REVERT: E 205 GLU cc_start: 0.7234 (pm20) cc_final: 0.6388 (mm-30) REVERT: H 149 ARG cc_start: 0.8623 (mtm180) cc_final: 0.7959 (mtm180) REVERT: H 205 GLU cc_start: 0.7320 (pm20) cc_final: 0.6346 (mm-30) outliers start: 53 outliers final: 38 residues processed: 364 average time/residue: 0.1358 time to fit residues: 79.3553 Evaluate side-chains 285 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 247 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 554 THR Chi-restraints excluded: chain C residue 556 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 271 ASN Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain H residue 26 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 150 optimal weight: 0.7980 chunk 162 optimal weight: 4.9990 chunk 206 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 203 optimal weight: 0.9980 chunk 250 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN C 143 ASN ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 GLN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN B 132 ASN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 GLN E 136 GLN E 150 GLN H 150 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.165054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.128240 restraints weight = 31672.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.124889 restraints weight = 24705.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.126841 restraints weight = 24192.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.127182 restraints weight = 15721.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.127662 restraints weight = 14743.793| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23056 Z= 0.132 Angle : 0.517 6.547 30984 Z= 0.279 Chirality : 0.044 0.159 3380 Planarity : 0.003 0.041 3952 Dihedral : 4.083 15.935 3000 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.22 % Favored : 95.64 % Rotamer: Outliers : 1.80 % Allowed : 12.92 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.16), residues: 2752 helix: 1.24 (0.16), residues: 1184 sheet: -1.66 (0.25), residues: 436 loop : -1.16 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 452 TYR 0.018 0.001 TYR C 278 PHE 0.026 0.001 PHE F 76 TRP 0.010 0.001 TRP B 126 HIS 0.008 0.001 HIS H 172 Details of bonding type rmsd covalent geometry : bond 0.00298 (23056) covalent geometry : angle 0.51703 (30984) hydrogen bonds : bond 0.03402 ( 976) hydrogen bonds : angle 5.20825 ( 2904) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 292 time to evaluate : 1.226 Fit side-chains REVERT: A 407 GLU cc_start: 0.7833 (tt0) cc_final: 0.7549 (tt0) REVERT: G 161 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7922 (mt) REVERT: F 78 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7076 (tm-30) REVERT: F 126 TYR cc_start: 0.2686 (m-10) cc_final: 0.2386 (m-10) REVERT: F 149 ARG cc_start: 0.8573 (mtm180) cc_final: 0.7915 (mtm180) REVERT: F 161 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7703 (mt) REVERT: F 208 ASN cc_start: 0.5769 (m110) cc_final: 0.5517 (m-40) REVERT: B 348 MET cc_start: 0.8289 (mmm) cc_final: 0.7877 (tpt) REVERT: E 149 ARG cc_start: 0.8532 (mtm180) cc_final: 0.8040 (mtm180) REVERT: E 161 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7701 (mt) REVERT: H 149 ARG cc_start: 0.8594 (mtm180) cc_final: 0.7927 (mtm180) REVERT: H 161 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7728 (mt) outliers start: 45 outliers final: 26 residues processed: 324 average time/residue: 0.1506 time to fit residues: 76.5621 Evaluate side-chains 266 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 236 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 556 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 271 ASN Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 161 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 199 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 191 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 272 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 chunk 224 optimal weight: 8.9990 chunk 142 optimal weight: 0.7980 chunk 133 optimal weight: 9.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 ASN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 ASN ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 GLN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 ASN B 143 ASN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 GLN B 551 ASN E 121 ASN E 136 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.154365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.117770 restraints weight = 32110.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.115047 restraints weight = 24361.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.116631 restraints weight = 23912.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.117065 restraints weight = 17361.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.117481 restraints weight = 15557.025| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 23056 Z= 0.359 Angle : 0.721 8.745 30984 Z= 0.383 Chirality : 0.051 0.180 3380 Planarity : 0.004 0.046 3952 Dihedral : 4.817 25.378 3000 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.01 % Favored : 92.77 % Rotamer: Outliers : 2.92 % Allowed : 14.60 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.16), residues: 2752 helix: 0.81 (0.15), residues: 1176 sheet: -1.90 (0.24), residues: 432 loop : -1.57 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 296 TYR 0.014 0.002 TYR C 278 PHE 0.024 0.003 PHE G 69 TRP 0.015 0.003 TRP C 126 HIS 0.008 0.001 HIS H 172 Details of bonding type rmsd covalent geometry : bond 0.00849 (23056) covalent geometry : angle 0.72061 (30984) hydrogen bonds : bond 0.04298 ( 976) hydrogen bonds : angle 5.61891 ( 2904) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 292 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ILE cc_start: 0.8427 (pt) cc_final: 0.8179 (pt) REVERT: G 56 GLU cc_start: 0.6110 (pp20) cc_final: 0.5857 (pp20) REVERT: G 162 ASP cc_start: 0.7485 (m-30) cc_final: 0.7131 (m-30) REVERT: C 27 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8901 (tt) REVERT: C 348 MET cc_start: 0.8402 (tpt) cc_final: 0.8156 (tpt) REVERT: F 149 ARG cc_start: 0.8626 (mtm180) cc_final: 0.7927 (mtm180) REVERT: D 348 MET cc_start: 0.8398 (tpt) cc_final: 0.8159 (tpt) REVERT: B 27 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8883 (tt) REVERT: E 136 GLN cc_start: 0.8306 (mt0) cc_final: 0.7430 (mp10) REVERT: H 149 ARG cc_start: 0.8624 (mtm180) cc_final: 0.7970 (mtm180) outliers start: 73 outliers final: 44 residues processed: 350 average time/residue: 0.1541 time to fit residues: 84.6770 Evaluate side-chains 274 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 228 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 TYR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 271 ASN Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain H residue 65 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 146 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 254 optimal weight: 10.0000 chunk 266 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 187 optimal weight: 0.7980 chunk 116 optimal weight: 10.0000 chunk 262 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 GLN C 551 ASN F 121 ASN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 GLN ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 GLN E 121 ASN H 136 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.160549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.124122 restraints weight = 31427.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.122550 restraints weight = 23065.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.124105 restraints weight = 22444.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.124604 restraints weight = 15795.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.125047 restraints weight = 14402.975| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23056 Z= 0.139 Angle : 0.540 6.107 30984 Z= 0.291 Chirality : 0.044 0.171 3380 Planarity : 0.003 0.040 3952 Dihedral : 4.360 19.571 3000 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.01 % Favored : 94.84 % Rotamer: Outliers : 2.16 % Allowed : 16.92 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.16), residues: 2752 helix: 1.03 (0.15), residues: 1180 sheet: -1.82 (0.24), residues: 472 loop : -1.32 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 83 TYR 0.015 0.001 TYR A 278 PHE 0.023 0.001 PHE F 76 TRP 0.010 0.002 TRP B 126 HIS 0.005 0.001 HIS F 172 Details of bonding type rmsd covalent geometry : bond 0.00321 (23056) covalent geometry : angle 0.54046 (30984) hydrogen bonds : bond 0.03322 ( 976) hydrogen bonds : angle 5.20625 ( 2904) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 301 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 MET cc_start: 0.8314 (mmm) cc_final: 0.7964 (tpp) REVERT: G 139 LEU cc_start: 0.8225 (tp) cc_final: 0.7992 (mp) REVERT: G 161 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8061 (mt) REVERT: G 203 GLU cc_start: 0.8092 (pt0) cc_final: 0.7778 (pt0) REVERT: G 205 GLU cc_start: 0.7468 (pm20) cc_final: 0.6575 (mm-30) REVERT: F 149 ARG cc_start: 0.8585 (mtm180) cc_final: 0.7926 (mtm180) REVERT: E 162 ASP cc_start: 0.7292 (m-30) cc_final: 0.6883 (m-30) REVERT: H 149 ARG cc_start: 0.8589 (mtm180) cc_final: 0.7961 (mtm180) outliers start: 54 outliers final: 31 residues processed: 344 average time/residue: 0.1557 time to fit residues: 84.4913 Evaluate side-chains 289 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 257 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 271 ASN Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 65 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 42 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 120 optimal weight: 0.4980 chunk 264 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN H 136 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.160661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.124066 restraints weight = 31698.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.122913 restraints weight = 21805.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.124233 restraints weight = 21682.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.124839 restraints weight = 15191.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.125182 restraints weight = 13814.201| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23056 Z= 0.147 Angle : 0.535 6.074 30984 Z= 0.287 Chirality : 0.044 0.161 3380 Planarity : 0.003 0.052 3952 Dihedral : 4.237 18.929 3000 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.45 % Favored : 94.40 % Rotamer: Outliers : 2.36 % Allowed : 17.04 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.16), residues: 2752 helix: 1.13 (0.16), residues: 1180 sheet: -1.81 (0.25), residues: 436 loop : -1.21 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 83 TYR 0.013 0.001 TYR A 278 PHE 0.037 0.001 PHE D 561 TRP 0.009 0.002 TRP B 126 HIS 0.005 0.001 HIS F 172 Details of bonding type rmsd covalent geometry : bond 0.00343 (23056) covalent geometry : angle 0.53481 (30984) hydrogen bonds : bond 0.03251 ( 976) hydrogen bonds : angle 5.13070 ( 2904) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 301 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8738 (tt) REVERT: A 348 MET cc_start: 0.8352 (mmm) cc_final: 0.7997 (tpp) REVERT: G 32 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7871 (mt-10) REVERT: G 203 GLU cc_start: 0.8032 (pt0) cc_final: 0.7770 (pt0) REVERT: G 205 GLU cc_start: 0.7411 (pm20) cc_final: 0.6710 (mm-30) REVERT: F 149 ARG cc_start: 0.8582 (mtm180) cc_final: 0.7903 (mtm180) REVERT: D 27 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8684 (tt) REVERT: E 136 GLN cc_start: 0.8073 (mt0) cc_final: 0.7334 (mp10) REVERT: E 161 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7814 (mt) REVERT: H 149 ARG cc_start: 0.8586 (mtm180) cc_final: 0.7832 (mtm180) REVERT: H 161 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7870 (mt) outliers start: 59 outliers final: 35 residues processed: 350 average time/residue: 0.1606 time to fit residues: 88.7793 Evaluate side-chains 305 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 266 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 40 TYR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 271 ASN Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 161 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 244 optimal weight: 20.0000 chunk 85 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 273 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 181 optimal weight: 0.9980 chunk 179 optimal weight: 10.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 GLN F 121 ASN F 136 GLN F 208 ASN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.157857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.121106 restraints weight = 31873.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.119183 restraints weight = 22474.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.120762 restraints weight = 22494.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.121252 restraints weight = 15885.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.121607 restraints weight = 14545.947| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23056 Z= 0.213 Angle : 0.586 7.113 30984 Z= 0.312 Chirality : 0.045 0.158 3380 Planarity : 0.004 0.053 3952 Dihedral : 4.403 21.012 3000 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.21 % Favored : 93.64 % Rotamer: Outliers : 2.32 % Allowed : 16.92 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.16), residues: 2752 helix: 1.02 (0.16), residues: 1180 sheet: -1.74 (0.25), residues: 436 loop : -1.28 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 296 TYR 0.022 0.001 TYR D 106 PHE 0.028 0.002 PHE A 561 TRP 0.010 0.002 TRP A 126 HIS 0.008 0.001 HIS E 172 Details of bonding type rmsd covalent geometry : bond 0.00505 (23056) covalent geometry : angle 0.58562 (30984) hydrogen bonds : bond 0.03477 ( 976) hydrogen bonds : angle 5.25791 ( 2904) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 275 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8794 (tt) REVERT: A 348 MET cc_start: 0.8314 (mmm) cc_final: 0.8042 (tpp) REVERT: G 205 GLU cc_start: 0.7538 (pm20) cc_final: 0.6741 (mm-30) REVERT: C 27 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8813 (tt) REVERT: F 161 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7937 (mt) REVERT: D 27 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8703 (tt) REVERT: B 27 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8808 (tt) REVERT: E 149 ARG cc_start: 0.8451 (mtm180) cc_final: 0.7979 (mtm180) REVERT: H 149 ARG cc_start: 0.8607 (mtm180) cc_final: 0.7878 (mtm180) REVERT: H 161 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7938 (mt) outliers start: 58 outliers final: 46 residues processed: 320 average time/residue: 0.1698 time to fit residues: 84.9587 Evaluate side-chains 320 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 268 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 40 TYR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 271 ASN Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 161 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 213 optimal weight: 3.9990 chunk 66 optimal weight: 0.0050 chunk 149 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 181 optimal weight: 10.0000 chunk 232 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 overall best weight: 2.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 ASN ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 ASN ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN H 136 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.157432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.120398 restraints weight = 31588.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.118928 restraints weight = 21840.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.120313 restraints weight = 21854.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.120867 restraints weight = 15640.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.121214 restraints weight = 14196.896| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 23056 Z= 0.205 Angle : 0.582 6.753 30984 Z= 0.309 Chirality : 0.046 0.161 3380 Planarity : 0.004 0.055 3952 Dihedral : 4.418 20.493 3000 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.21 % Favored : 93.60 % Rotamer: Outliers : 2.52 % Allowed : 17.44 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.16), residues: 2752 helix: 0.96 (0.16), residues: 1180 sheet: -1.60 (0.26), residues: 416 loop : -1.22 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 83 TYR 0.014 0.001 TYR D 106 PHE 0.026 0.002 PHE A 561 TRP 0.010 0.002 TRP A 126 HIS 0.005 0.001 HIS F 172 Details of bonding type rmsd covalent geometry : bond 0.00487 (23056) covalent geometry : angle 0.58168 (30984) hydrogen bonds : bond 0.03463 ( 976) hydrogen bonds : angle 5.22378 ( 2904) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 279 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8795 (tt) REVERT: A 348 MET cc_start: 0.8316 (mmm) cc_final: 0.8056 (tpp) REVERT: G 203 GLU cc_start: 0.8061 (pt0) cc_final: 0.7771 (pt0) REVERT: G 205 GLU cc_start: 0.7540 (pm20) cc_final: 0.6526 (mm-30) REVERT: C 27 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8828 (tt) REVERT: F 55 LYS cc_start: 0.7994 (mmtt) cc_final: 0.7639 (mmtp) REVERT: F 136 GLN cc_start: 0.7803 (mt0) cc_final: 0.7222 (mp10) REVERT: F 149 ARG cc_start: 0.8604 (mtm180) cc_final: 0.7864 (mtm180) REVERT: F 161 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7920 (mt) REVERT: F 181 GLN cc_start: 0.8401 (mp10) cc_final: 0.8084 (mp10) REVERT: D 27 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8701 (tt) REVERT: B 27 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8813 (tt) REVERT: E 136 GLN cc_start: 0.8093 (mt0) cc_final: 0.7379 (mp10) REVERT: E 149 ARG cc_start: 0.8473 (mtm180) cc_final: 0.7993 (mtm180) REVERT: H 55 LYS cc_start: 0.8022 (mmtt) cc_final: 0.7661 (mmtp) REVERT: H 136 GLN cc_start: 0.8002 (mt0) cc_final: 0.7357 (mp10) REVERT: H 161 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7907 (mt) REVERT: H 181 GLN cc_start: 0.8387 (mp10) cc_final: 0.8117 (mp10) outliers start: 63 outliers final: 50 residues processed: 330 average time/residue: 0.1702 time to fit residues: 88.0748 Evaluate side-chains 319 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 263 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 40 TYR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 554 THR Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 271 ASN Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 161 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 50 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 235 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.156671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.119705 restraints weight = 31776.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.118228 restraints weight = 23759.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.119690 restraints weight = 22489.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.120104 restraints weight = 16420.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.120486 restraints weight = 14804.559| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 23056 Z= 0.222 Angle : 0.601 7.173 30984 Z= 0.319 Chirality : 0.046 0.160 3380 Planarity : 0.004 0.056 3952 Dihedral : 4.462 20.300 3000 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.54 % Favored : 93.24 % Rotamer: Outliers : 2.56 % Allowed : 18.04 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.16), residues: 2752 helix: 0.91 (0.16), residues: 1180 sheet: -1.58 (0.26), residues: 416 loop : -1.24 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 83 TYR 0.014 0.001 TYR D 106 PHE 0.025 0.002 PHE A 561 TRP 0.010 0.002 TRP A 126 HIS 0.005 0.001 HIS F 172 Details of bonding type rmsd covalent geometry : bond 0.00528 (23056) covalent geometry : angle 0.60094 (30984) hydrogen bonds : bond 0.03548 ( 976) hydrogen bonds : angle 5.25747 ( 2904) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 265 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8803 (tt) REVERT: A 341 LYS cc_start: 0.7427 (tmtt) cc_final: 0.6829 (ptmm) REVERT: A 348 MET cc_start: 0.8302 (mmm) cc_final: 0.8066 (tpp) REVERT: G 55 LYS cc_start: 0.7968 (mmmt) cc_final: 0.7355 (mmtp) REVERT: G 205 GLU cc_start: 0.7571 (pm20) cc_final: 0.6487 (mm-30) REVERT: C 27 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8835 (tt) REVERT: F 161 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7957 (mt) REVERT: D 27 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8715 (tt) REVERT: D 341 LYS cc_start: 0.7445 (tmtt) cc_final: 0.6842 (ptmm) REVERT: B 27 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8838 (tt) REVERT: E 149 ARG cc_start: 0.8462 (mtm180) cc_final: 0.7967 (mtm180) REVERT: H 161 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7956 (mt) outliers start: 64 outliers final: 50 residues processed: 316 average time/residue: 0.1663 time to fit residues: 82.3615 Evaluate side-chains 324 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 268 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 40 TYR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 554 THR Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 271 ASN Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain H residue 161 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 7 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 179 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 126 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 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 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 ASN ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 ASN ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN H 136 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.161014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.123525 restraints weight = 31669.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.122447 restraints weight = 21732.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.123767 restraints weight = 21560.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.124341 restraints weight = 15341.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.124818 restraints weight = 13830.446| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23056 Z= 0.127 Angle : 0.567 14.527 30984 Z= 0.297 Chirality : 0.044 0.163 3380 Planarity : 0.003 0.057 3952 Dihedral : 4.261 16.799 3000 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.54 % Favored : 95.31 % Rotamer: Outliers : 1.72 % Allowed : 18.76 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.16), residues: 2752 helix: 1.02 (0.16), residues: 1180 sheet: -1.55 (0.24), residues: 472 loop : -1.15 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 332 TYR 0.012 0.001 TYR D 106 PHE 0.024 0.001 PHE A 561 TRP 0.009 0.001 TRP A 126 HIS 0.010 0.001 HIS H 172 Details of bonding type rmsd covalent geometry : bond 0.00290 (23056) covalent geometry : angle 0.56712 (30984) hydrogen bonds : bond 0.03227 ( 976) hydrogen bonds : angle 5.08961 ( 2904) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 296 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8579 (tt) REVERT: A 348 MET cc_start: 0.8336 (mmm) cc_final: 0.8035 (tpp) REVERT: G 55 LYS cc_start: 0.8036 (mmmt) cc_final: 0.7475 (mmtp) REVERT: G 163 GLU cc_start: 0.7985 (pm20) cc_final: 0.7629 (pm20) REVERT: C 27 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8674 (tt) REVERT: C 53 PHE cc_start: 0.8549 (m-10) cc_final: 0.8165 (m-10) REVERT: F 136 GLN cc_start: 0.7795 (mt0) cc_final: 0.7205 (mp10) REVERT: F 149 ARG cc_start: 0.8513 (mtm180) cc_final: 0.7854 (mtm180) REVERT: D 53 PHE cc_start: 0.8573 (m-10) cc_final: 0.8173 (m-10) REVERT: B 27 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8637 (tt) REVERT: B 53 PHE cc_start: 0.8551 (m-10) cc_final: 0.8173 (m-10) REVERT: E 136 GLN cc_start: 0.8063 (mt0) cc_final: 0.7364 (mp10) REVERT: E 149 ARG cc_start: 0.8443 (mtm180) cc_final: 0.8142 (mtm180) REVERT: H 55 LYS cc_start: 0.8071 (mmtt) cc_final: 0.7685 (mmtp) REVERT: H 136 GLN cc_start: 0.7830 (mt0) cc_final: 0.7227 (mp10) REVERT: H 149 ARG cc_start: 0.8555 (mtm180) cc_final: 0.7843 (mtm180) REVERT: H 161 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7796 (mt) outliers start: 43 outliers final: 36 residues processed: 327 average time/residue: 0.1577 time to fit residues: 80.9046 Evaluate side-chains 311 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 271 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 40 TYR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 271 ASN Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain H residue 161 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 160 optimal weight: 1.9990 chunk 156 optimal weight: 0.1980 chunk 229 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 173 optimal weight: 0.0060 chunk 226 optimal weight: 0.9980 chunk 194 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 chunk 272 optimal weight: 9.9990 chunk 191 optimal weight: 0.0570 chunk 200 optimal weight: 3.9990 overall best weight: 0.6516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 ASN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.161802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.125076 restraints weight = 31514.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.121390 restraints weight = 24252.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.123140 restraints weight = 24234.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.123633 restraints weight = 16491.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.124059 restraints weight = 14784.250| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23056 Z= 0.124 Angle : 0.580 11.040 30984 Z= 0.303 Chirality : 0.044 0.167 3380 Planarity : 0.003 0.058 3952 Dihedral : 4.221 16.357 3000 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.80 % Favored : 95.06 % Rotamer: Outliers : 1.64 % Allowed : 19.56 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.17), residues: 2752 helix: 1.05 (0.16), residues: 1184 sheet: -1.57 (0.25), residues: 436 loop : -1.04 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 83 TYR 0.014 0.001 TYR D 493 PHE 0.024 0.001 PHE A 561 TRP 0.012 0.001 TRP A 126 HIS 0.003 0.001 HIS F 172 Details of bonding type rmsd covalent geometry : bond 0.00281 (23056) covalent geometry : angle 0.57996 (30984) hydrogen bonds : bond 0.03146 ( 976) hydrogen bonds : angle 5.04143 ( 2904) =============================================================================== Job complete usr+sys time: 3363.19 seconds wall clock time: 59 minutes 42.52 seconds (3582.52 seconds total)