Starting phenix.real_space_refine on Wed May 21 20:05:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j4t_35977/05_2025/8j4t_35977.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j4t_35977/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j4t_35977/05_2025/8j4t_35977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j4t_35977/05_2025/8j4t_35977.map" model { file = "/net/cci-nas-00/data/ceres_data/8j4t_35977/05_2025/8j4t_35977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j4t_35977/05_2025/8j4t_35977.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 12.82, per 1000 atoms: 0.57 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: 5.94 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 2.68 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: 7.78 Time building geometry restraints manager: 6.93 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: 0.18 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'F' 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.980 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 50.200 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.100 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.870 ------------------------------------------------------------------------------- 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 : 10.72 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.17), 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 TRP 0.014 0.002 TRP D 126 HIS 0.002 0.001 HIS G 172 PHE 0.024 0.001 PHE F 207 TYR 0.008 0.001 TYR A 312 ARG 0.007 0.001 ARG B 526 Details of bonding type rmsd hydrogen bonds : bond 0.18594 ( 976) hydrogen bonds : angle 7.32843 ( 2904) covalent geometry : bond 0.00222 (23056) covalent geometry : angle 0.53605 (30984) *********************** 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 : 2.501 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: 0.3356 time to fit residues: 250.2062 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 : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 8.9990 chunk 209 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 216 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 131 optimal weight: 7.9990 chunk 161 optimal weight: 0.9980 chunk 250 optimal weight: 8.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 330 ASN C 538 GLN F 121 ASN ** 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 330 ASN B 538 GLN E 150 GLN ** E 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.169241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.133352 restraints weight = 31544.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.129453 restraints weight = 25506.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.131647 restraints weight = 22306.798| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23056 Z= 0.177 Angle : 0.570 7.014 30984 Z= 0.303 Chirality : 0.045 0.160 3380 Planarity : 0.003 0.046 3952 Dihedral : 4.070 16.691 3000 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.38 % Favored : 94.48 % Rotamer: Outliers : 1.76 % Allowed : 8.64 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2752 helix: 1.34 (0.16), residues: 1184 sheet: -1.49 (0.26), residues: 436 loop : -1.07 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 126 HIS 0.005 0.001 HIS E 172 PHE 0.018 0.002 PHE F 76 TYR 0.011 0.001 TYR E 126 ARG 0.004 0.001 ARG C 452 Details of bonding type rmsd hydrogen bonds : bond 0.03662 ( 976) hydrogen bonds : angle 5.40392 ( 2904) covalent geometry : bond 0.00408 (23056) covalent geometry : angle 0.57026 (30984) *********************** 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 374 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 330 time to evaluate : 2.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 161 ILE cc_start: 0.8103 (mt) cc_final: 0.7893 (mt) REVERT: G 205 GLU cc_start: 0.7285 (pm20) cc_final: 0.6244 (mm-30) REVERT: F 63 TYR cc_start: 0.7848 (t80) cc_final: 0.7470 (t80) REVERT: F 161 ILE cc_start: 0.8036 (mt) cc_final: 0.7789 (mt) REVERT: E 149 ARG cc_start: 0.8583 (mtm180) cc_final: 0.7957 (mtm180) REVERT: E 205 GLU cc_start: 0.7210 (pm20) cc_final: 0.6363 (mm-30) REVERT: H 161 ILE cc_start: 0.8152 (mt) cc_final: 0.7908 (mt) outliers start: 44 outliers final: 34 residues processed: 360 average time/residue: 0.3371 time to fit residues: 191.1906 Evaluate side-chains 305 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 271 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 294 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 C residue 93 VAL Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 294 LEU 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 24 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 294 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 271 ASN Chi-restraints excluded: chain B residue 294 LEU 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 H residue 24 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 20 optimal weight: 3.9990 chunk 268 optimal weight: 0.8980 chunk 212 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 96 optimal weight: 0.0020 chunk 105 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- 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 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** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 H 136 GLN H 150 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.166461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.129901 restraints weight = 31341.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.125998 restraints weight = 23330.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.127862 restraints weight = 21820.777| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23056 Z= 0.146 Angle : 0.512 5.461 30984 Z= 0.277 Chirality : 0.044 0.159 3380 Planarity : 0.003 0.042 3952 Dihedral : 3.944 15.856 3000 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.36 % Favored : 95.49 % Rotamer: Outliers : 1.76 % Allowed : 11.96 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.17), residues: 2752 helix: 1.32 (0.16), residues: 1184 sheet: -1.34 (0.24), residues: 472 loop : -1.17 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 126 HIS 0.005 0.001 HIS H 172 PHE 0.018 0.001 PHE F 76 TYR 0.009 0.001 TYR G 126 ARG 0.005 0.001 ARG C 452 Details of bonding type rmsd hydrogen bonds : bond 0.03378 ( 976) hydrogen bonds : angle 5.13573 ( 2904) covalent geometry : bond 0.00337 (23056) covalent geometry : angle 0.51217 (30984) *********************** 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 328 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 284 time to evaluate : 2.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 MET cc_start: 0.8266 (mmm) cc_final: 0.7919 (tpt) REVERT: C 348 MET cc_start: 0.8290 (mmm) cc_final: 0.7960 (tpt) REVERT: F 78 GLU cc_start: 0.7392 (tm-30) cc_final: 0.6971 (tm-30) REVERT: F 149 ARG cc_start: 0.8596 (mtm180) cc_final: 0.7966 (mtm180) REVERT: D 348 MET cc_start: 0.8246 (mmm) cc_final: 0.7897 (tpt) REVERT: B 348 MET cc_start: 0.8284 (mmm) cc_final: 0.7953 (tpt) REVERT: H 149 ARG cc_start: 0.8597 (mtm180) cc_final: 0.7963 (mtm180) REVERT: H 205 GLU cc_start: 0.7329 (pm20) cc_final: 0.6422 (mm-30) outliers start: 44 outliers final: 29 residues processed: 313 average time/residue: 0.3326 time to fit residues: 164.3991 Evaluate side-chains 284 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 255 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 294 LEU 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 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 294 LEU 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 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 294 LEU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain B residue 271 ASN Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 43 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 172 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 246 optimal weight: 0.8980 chunk 134 optimal weight: 10.0000 chunk 193 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 231 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 224 optimal weight: 9.9990 chunk 186 optimal weight: 0.4980 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 143 ASN ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 GLN F 208 ASN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 538 GLN E 136 GLN E 150 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.161289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.123624 restraints weight = 32116.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.122379 restraints weight = 25298.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.123911 restraints weight = 23159.099| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 23056 Z= 0.204 Angle : 0.558 5.761 30984 Z= 0.301 Chirality : 0.045 0.178 3380 Planarity : 0.003 0.040 3952 Dihedral : 4.184 16.710 3000 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.60 % Favored : 94.26 % Rotamer: Outliers : 2.52 % Allowed : 12.48 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.16), residues: 2752 helix: 1.20 (0.16), residues: 1184 sheet: -1.61 (0.24), residues: 476 loop : -1.27 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 126 HIS 0.004 0.001 HIS E 172 PHE 0.018 0.002 PHE F 76 TYR 0.010 0.001 TYR D 314 ARG 0.005 0.001 ARG F 83 Details of bonding type rmsd hydrogen bonds : bond 0.03492 ( 976) hydrogen bonds : angle 5.18813 ( 2904) covalent geometry : bond 0.00482 (23056) covalent geometry : angle 0.55773 (30984) *********************** 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 382 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 319 time to evaluate : 2.802 Fit side-chains revert: symmetry clash REVERT: A 348 MET cc_start: 0.8234 (mmm) cc_final: 0.7930 (tpt) REVERT: G 149 ARG cc_start: 0.8583 (mtm180) cc_final: 0.8042 (mtm180) REVERT: C 348 MET cc_start: 0.8259 (mmm) cc_final: 0.7959 (tpt) REVERT: F 149 ARG cc_start: 0.8607 (mtm180) cc_final: 0.7953 (mtm180) REVERT: F 161 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7746 (mt) REVERT: D 348 MET cc_start: 0.8234 (mmm) cc_final: 0.7934 (tpt) REVERT: B 348 MET cc_start: 0.8253 (mmm) cc_final: 0.7970 (tpp) REVERT: H 149 ARG cc_start: 0.8644 (mtm180) cc_final: 0.7928 (mtm180) REVERT: H 161 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7825 (mt) REVERT: H 205 GLU cc_start: 0.7420 (pm20) cc_final: 0.6356 (mm-30) outliers start: 63 outliers final: 41 residues processed: 363 average time/residue: 0.3556 time to fit residues: 202.9158 Evaluate side-chains 319 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 276 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 65 THR 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 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 139 LEU 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 271 ASN Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 378 ILE 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 43 SER Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 161 ILE 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 271 ASN Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 526 ARG 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 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 26 ILE Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 161 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 144 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 231 optimal weight: 0.1980 chunk 22 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 chunk 201 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 538 GLN ** 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 ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 GLN E 136 GLN H 136 GLN H 150 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.163564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.126282 restraints weight = 31734.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.125171 restraints weight = 21994.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.126568 restraints weight = 21768.006| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23056 Z= 0.133 Angle : 0.511 7.210 30984 Z= 0.276 Chirality : 0.043 0.160 3380 Planarity : 0.003 0.049 3952 Dihedral : 4.041 15.578 3000 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.36 % Favored : 95.49 % Rotamer: Outliers : 2.64 % Allowed : 13.84 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.17), residues: 2752 helix: 1.26 (0.16), residues: 1184 sheet: -1.45 (0.24), residues: 472 loop : -1.15 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 126 HIS 0.004 0.001 HIS H 172 PHE 0.024 0.001 PHE H 76 TYR 0.016 0.001 TYR C 278 ARG 0.004 0.000 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.03127 ( 976) hydrogen bonds : angle 5.04019 ( 2904) covalent geometry : bond 0.00307 (23056) covalent geometry : angle 0.51114 (30984) *********************** 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 360 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 294 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 MET cc_start: 0.8229 (mmm) cc_final: 0.8006 (tpp) REVERT: C 348 MET cc_start: 0.8255 (mmm) cc_final: 0.8040 (tpp) REVERT: F 149 ARG cc_start: 0.8538 (mtm180) cc_final: 0.7893 (mtm180) REVERT: F 161 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7709 (mt) REVERT: D 348 MET cc_start: 0.8238 (mmm) cc_final: 0.8029 (tpp) REVERT: B 348 MET cc_start: 0.8247 (mmm) cc_final: 0.8030 (tpp) REVERT: H 149 ARG cc_start: 0.8575 (mtm180) cc_final: 0.7917 (mtm180) REVERT: H 161 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7763 (mt) outliers start: 66 outliers final: 45 residues processed: 346 average time/residue: 0.3351 time to fit residues: 181.4900 Evaluate side-chains 325 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 278 time to evaluate : 2.515 ------------------------------------------------------------------------------- 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 378 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 214 SER 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 331 THR Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 556 ASP Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 214 SER 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 331 THR 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 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 B residue 556 ASP Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 161 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 221 optimal weight: 10.0000 chunk 96 optimal weight: 0.5980 chunk 203 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 224 optimal weight: 10.0000 chunk 159 optimal weight: 0.6980 chunk 250 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 538 GLN ** 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 ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 GLN E 136 GLN H 208 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.161199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.123652 restraints weight = 31587.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.122322 restraints weight = 23719.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.123805 restraints weight = 22566.374| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23056 Z= 0.168 Angle : 0.536 6.333 30984 Z= 0.289 Chirality : 0.044 0.164 3380 Planarity : 0.003 0.052 3952 Dihedral : 4.140 17.432 3000 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.85 % Favored : 94.00 % Rotamer: Outliers : 2.12 % Allowed : 15.36 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.17), residues: 2752 helix: 1.24 (0.16), residues: 1184 sheet: -1.50 (0.24), residues: 472 loop : -1.16 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 126 HIS 0.006 0.001 HIS E 172 PHE 0.018 0.001 PHE G 76 TYR 0.014 0.001 TYR C 278 ARG 0.003 0.000 ARG D 452 Details of bonding type rmsd hydrogen bonds : bond 0.03224 ( 976) hydrogen bonds : angle 5.08735 ( 2904) covalent geometry : bond 0.00395 (23056) covalent geometry : angle 0.53600 (30984) *********************** 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 336 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 283 time to evaluate : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 MET cc_start: 0.8240 (mmm) cc_final: 0.7924 (tpp) REVERT: G 149 ARG cc_start: 0.8568 (mtm180) cc_final: 0.7990 (mtm180) REVERT: C 348 MET cc_start: 0.8270 (mmm) cc_final: 0.7958 (tpp) REVERT: F 149 ARG cc_start: 0.8570 (mtm180) cc_final: 0.7871 (mtm180) REVERT: F 161 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7749 (mt) REVERT: D 348 MET cc_start: 0.8237 (mmm) cc_final: 0.7951 (tpp) REVERT: B 348 MET cc_start: 0.8256 (mmm) cc_final: 0.7948 (tpp) REVERT: H 136 GLN cc_start: 0.8065 (mt0) cc_final: 0.7277 (mp10) REVERT: H 149 ARG cc_start: 0.8593 (mtm180) cc_final: 0.7871 (mtm180) REVERT: H 161 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7797 (mt) outliers start: 53 outliers final: 41 residues processed: 319 average time/residue: 0.3495 time to fit residues: 175.3130 Evaluate side-chains 301 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 258 time to evaluate : 2.629 ------------------------------------------------------------------------------- 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 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 139 LEU 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 271 ASN Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 161 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 130 LEU Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain B residue 40 TYR 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 456 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain H residue 43 SER 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 8 optimal weight: 6.9990 chunk 260 optimal weight: 9.9990 chunk 224 optimal weight: 7.9990 chunk 96 optimal weight: 0.0970 chunk 145 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 219 optimal weight: 0.9990 chunk 213 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 274 optimal weight: 9.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 GLN E 121 ASN E 136 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.158780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.121598 restraints weight = 31805.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.120033 restraints weight = 25233.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.121493 restraints weight = 24090.921| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3900 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= 0.201 Angle : 0.568 6.327 30984 Z= 0.305 Chirality : 0.045 0.166 3380 Planarity : 0.004 0.056 3952 Dihedral : 4.242 21.025 3000 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.63 % Favored : 94.22 % Rotamer: Outliers : 2.36 % Allowed : 16.28 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.16), residues: 2752 helix: 1.11 (0.16), residues: 1184 sheet: -1.59 (0.24), residues: 472 loop : -1.18 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 126 HIS 0.006 0.001 HIS E 172 PHE 0.019 0.002 PHE G 76 TYR 0.017 0.001 TYR D 493 ARG 0.005 0.000 ARG E 83 Details of bonding type rmsd hydrogen bonds : bond 0.03366 ( 976) hydrogen bonds : angle 5.12962 ( 2904) covalent geometry : bond 0.00474 (23056) covalent geometry : angle 0.56804 (30984) *********************** 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 346 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 287 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 149 ARG cc_start: 0.8576 (mtm180) cc_final: 0.7976 (mtm180) REVERT: F 136 GLN cc_start: 0.7928 (mt0) cc_final: 0.7230 (mp10) REVERT: F 149 ARG cc_start: 0.8577 (mtm180) cc_final: 0.7862 (mtm180) REVERT: F 161 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7822 (mt) REVERT: E 126 TYR cc_start: 0.3916 (m-80) cc_final: 0.3435 (m-80) REVERT: H 161 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7863 (mt) outliers start: 59 outliers final: 40 residues processed: 330 average time/residue: 0.3380 time to fit residues: 173.9361 Evaluate side-chains 302 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 260 time to evaluate : 2.539 ------------------------------------------------------------------------------- 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 271 ASN Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 526 ARG 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 271 ASN Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 161 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 331 THR Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 526 ARG Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 271 ASN Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 141 ILE 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 66 optimal weight: 0.5980 chunk 108 optimal weight: 0.0570 chunk 196 optimal weight: 8.9990 chunk 197 optimal weight: 0.9990 chunk 267 optimal weight: 0.9980 chunk 136 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 216 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 224 optimal weight: 0.0000 chunk 175 optimal weight: 5.9990 overall best weight: 0.4702 ------------------------------------------------------------------------------- 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 551 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** F 136 GLN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 ASN E 121 ASN E 136 GLN H 136 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.164205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.127796 restraints weight = 31475.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.124720 restraints weight = 25521.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.126254 restraints weight = 24627.944| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23056 Z= 0.110 Angle : 0.514 7.355 30984 Z= 0.278 Chirality : 0.043 0.157 3380 Planarity : 0.003 0.060 3952 Dihedral : 4.037 15.903 3000 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.29 % Favored : 95.57 % Rotamer: Outliers : 1.56 % Allowed : 17.16 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.17), residues: 2752 helix: 1.19 (0.16), residues: 1192 sheet: -1.35 (0.25), residues: 452 loop : -1.03 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 126 HIS 0.005 0.001 HIS E 172 PHE 0.020 0.001 PHE G 76 TYR 0.011 0.001 TYR A 416 ARG 0.004 0.000 ARG E 83 Details of bonding type rmsd hydrogen bonds : bond 0.02959 ( 976) hydrogen bonds : angle 4.94320 ( 2904) covalent geometry : bond 0.00241 (23056) covalent geometry : angle 0.51376 (30984) *********************** 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 332 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 293 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 149 ARG cc_start: 0.8553 (mtm180) cc_final: 0.7848 (mtm180) REVERT: F 161 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7526 (mt) REVERT: E 126 TYR cc_start: 0.4079 (m-80) cc_final: 0.3733 (m-80) REVERT: E 136 GLN cc_start: 0.8087 (mt0) cc_final: 0.7330 (mp10) REVERT: H 149 ARG cc_start: 0.8593 (mtm180) cc_final: 0.7849 (mtm180) REVERT: H 161 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7581 (mt) outliers start: 39 outliers final: 32 residues processed: 321 average time/residue: 0.3374 time to fit residues: 168.8588 Evaluate side-chains 313 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 279 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 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 88 ASP Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 93 VAL 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 43 SER Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain D residue 40 TYR 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 378 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 271 ASN Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 456 LEU 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 43 SER Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain H residue 43 SER 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 98 optimal weight: 0.0980 chunk 172 optimal weight: 5.9990 chunk 58 optimal weight: 20.0000 chunk 192 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 185 optimal weight: 0.6980 chunk 249 optimal weight: 8.9990 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 227 optimal weight: 0.3980 chunk 123 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 121 ASN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 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 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.166404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.130307 restraints weight = 31677.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.128033 restraints weight = 23235.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.129706 restraints weight = 23133.144| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3819 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= 0.115 Angle : 0.532 7.640 30984 Z= 0.287 Chirality : 0.043 0.159 3380 Planarity : 0.003 0.062 3952 Dihedral : 4.020 16.744 3000 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.54 % Favored : 95.31 % Rotamer: Outliers : 1.80 % Allowed : 17.80 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.17), residues: 2752 helix: 1.24 (0.16), residues: 1184 sheet: -1.19 (0.25), residues: 452 loop : -1.00 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 126 HIS 0.007 0.001 HIS G 172 PHE 0.043 0.001 PHE B 561 TYR 0.016 0.001 TYR C 493 ARG 0.008 0.000 ARG D 43 Details of bonding type rmsd hydrogen bonds : bond 0.02943 ( 976) hydrogen bonds : angle 4.89694 ( 2904) covalent geometry : bond 0.00258 (23056) covalent geometry : angle 0.53221 (30984) *********************** 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 353 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 308 time to evaluate : 2.646 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 30 MET cc_start: 0.7365 (mmp) cc_final: 0.7014 (mmp) REVERT: C 30 MET cc_start: 0.7255 (mmp) cc_final: 0.6885 (mmp) REVERT: F 136 GLN cc_start: 0.7824 (mt0) cc_final: 0.7228 (mp10) REVERT: F 149 ARG cc_start: 0.8530 (mtm180) cc_final: 0.7822 (mtm180) REVERT: F 161 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7525 (mt) REVERT: D 30 MET cc_start: 0.7361 (mmp) cc_final: 0.7002 (mmp) REVERT: E 126 TYR cc_start: 0.3908 (m-80) cc_final: 0.3413 (m-80) REVERT: E 149 ARG cc_start: 0.8437 (mtm180) cc_final: 0.8120 (mtm180) REVERT: H 136 GLN cc_start: 0.7968 (mt0) cc_final: 0.7197 (mp10) REVERT: H 161 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7580 (mt) outliers start: 45 outliers final: 35 residues processed: 336 average time/residue: 0.3339 time to fit residues: 176.1002 Evaluate side-chains 321 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 284 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 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 88 ASP Chi-restraints excluded: chain G residue 121 ASN Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 161 ILE 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 271 ASN Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain B residue 40 TYR 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 456 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 141 ILE 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 110 optimal weight: 10.0000 chunk 272 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 203 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 197 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 121 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** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** 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 = 0.3976 r_free = 0.3976 target = 0.159532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.122635 restraints weight = 31759.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.120742 restraints weight = 22983.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.122348 restraints weight = 22541.990| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 23056 Z= 0.196 Angle : 0.599 8.416 30984 Z= 0.322 Chirality : 0.045 0.169 3380 Planarity : 0.004 0.065 3952 Dihedral : 4.218 19.385 3000 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.96 % Favored : 93.97 % Rotamer: Outliers : 1.60 % Allowed : 18.64 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.16), residues: 2752 helix: 1.14 (0.16), residues: 1184 sheet: -1.34 (0.25), residues: 448 loop : -1.13 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 126 HIS 0.005 0.001 HIS A 415 PHE 0.036 0.002 PHE C 561 TYR 0.017 0.001 TYR C 106 ARG 0.009 0.001 ARG D 43 Details of bonding type rmsd hydrogen bonds : bond 0.03279 ( 976) hydrogen bonds : angle 5.07038 ( 2904) covalent geometry : bond 0.00465 (23056) covalent geometry : angle 0.59870 (30984) ********************** 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 334 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 294 time to evaluate : 2.852 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: G 149 ARG cc_start: 0.8544 (mtm180) cc_final: 0.7906 (mtm180) REVERT: F 161 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7701 (mt) REVERT: D 30 MET cc_start: 0.7623 (mmp) cc_final: 0.7330 (mmp) REVERT: E 126 TYR cc_start: 0.4054 (m-80) cc_final: 0.3848 (m-80) REVERT: E 136 GLN cc_start: 0.8119 (mt0) cc_final: 0.7364 (mp10) REVERT: E 149 ARG cc_start: 0.8489 (mtm180) cc_final: 0.7994 (mtm180) REVERT: E 203 GLU cc_start: 0.7947 (pt0) cc_final: 0.7653 (pt0) REVERT: E 205 GLU cc_start: 0.7483 (pm20) cc_final: 0.6804 (mm-30) REVERT: H 136 GLN cc_start: 0.8065 (mt0) cc_final: 0.7270 (mp10) REVERT: H 161 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7672 (mt) REVERT: H 163 GLU cc_start: 0.7765 (pm20) cc_final: 0.7535 (pm20) outliers start: 40 outliers final: 32 residues processed: 320 average time/residue: 0.3523 time to fit residues: 174.0965 Evaluate side-chains 319 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 285 time to evaluate : 2.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 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 G residue 121 ASN Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 161 ILE 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 271 ASN Chi-restraints excluded: chain D residue 331 THR 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 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 43 SER Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain H residue 43 SER 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 121 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 220 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 chunk 244 optimal weight: 0.0470 chunk 141 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 overall best weight: 1.6084 ------------------------------------------------------------------------------- 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 121 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** F 136 GLN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** 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 121 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.160634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.123477 restraints weight = 31546.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.123178 restraints weight = 22484.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.124528 restraints weight = 20545.211| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23056 Z= 0.158 Angle : 0.578 7.853 30984 Z= 0.310 Chirality : 0.044 0.169 3380 Planarity : 0.004 0.067 3952 Dihedral : 4.159 18.091 3000 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.72 % Allowed : 18.72 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.17), residues: 2752 helix: 1.09 (0.16), residues: 1188 sheet: -1.38 (0.24), residues: 472 loop : -1.07 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 126 HIS 0.006 0.001 HIS A 415 PHE 0.035 0.002 PHE B 561 TYR 0.013 0.001 TYR C 106 ARG 0.008 0.000 ARG D 43 Details of bonding type rmsd hydrogen bonds : bond 0.03136 ( 976) hydrogen bonds : angle 5.01058 ( 2904) covalent geometry : bond 0.00372 (23056) covalent geometry : angle 0.57794 (30984) =============================================================================== Job complete usr+sys time: 6564.05 seconds wall clock time: 117 minutes 7.81 seconds (7027.81 seconds total)