Starting phenix.real_space_refine on Tue Mar 19 00:41:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j4t_35977/03_2024/8j4t_35977.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j4t_35977/03_2024/8j4t_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j4t_35977/03_2024/8j4t_35977.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j4t_35977/03_2024/8j4t_35977.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j4t_35977/03_2024/8j4t_35977.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j4t_35977/03_2024/8j4t_35977.pdb" } 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 Residue "A PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 114": "OD1" <-> "OD2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 509": "OE1" <-> "OE2" Residue "G GLU 37": "OE1" <-> "OE2" Residue "G PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 162": "OD1" <-> "OD2" Residue "G PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 212": "OE1" <-> "OE2" Residue "C PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 114": "OD1" <-> "OD2" Residue "C PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 509": "OE1" <-> "OE2" Residue "F GLU 37": "OE1" <-> "OE2" Residue "F PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 162": "OD1" <-> "OD2" Residue "F PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 212": "OE1" <-> "OE2" Residue "D PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 114": "OD1" <-> "OD2" Residue "D PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 509": "OE1" <-> "OE2" Residue "B PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 114": "OD1" <-> "OD2" Residue "B PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 509": "OE1" <-> "OE2" Residue "E GLU 37": "OE1" <-> "OE2" Residue "E PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 162": "OD1" <-> "OD2" Residue "E PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "H GLU 37": "OE1" <-> "OE2" Residue "H PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 162": "OD1" <-> "OD2" Residue "H PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 212": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 11.15, per 1000 atoms: 0.49 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 - 3.50 Amino acid : False - 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: 8.32 Conformation dependent library (CDL) restraints added in 4.0 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: 2.45 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: 7.67 Time building geometry restraints manager: 9.05 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: 100.13 - 106.90: 335 106.90 - 113.67: 12475 113.67 - 120.44: 9096 120.44 - 127.21: 8962 127.21 - 133.99: 116 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 2.440 nonbonded pdb=" O LEU H 210 " pdb=" OG SER H 214 " model vdw 2.190 2.440 nonbonded pdb=" O LEU F 210 " pdb=" OG SER F 214 " model vdw 2.190 2.440 nonbonded pdb=" O LEU E 210 " pdb=" OG SER E 214 " model vdw 2.191 2.440 nonbonded pdb=" O TYR F 164 " pdb=" OG SER F 167 " model vdw 2.234 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.270 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 57.110 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.150 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.160 ------------------------------------------------------------------------------- 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= 0.143 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 483 time to evaluate : 2.955 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: 0.3387 time to fit residues: 252.7004 Evaluate side-chains 281 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 2.398 ------------------------------------------------------------------------------- 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: 10.0000 chunk 209 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 216 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 161 optimal weight: 1.9990 chunk 250 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 ** A 483 ASN ** 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 330 ASN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 GLN F 121 ASN F 213 ASN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN ** D 483 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 330 ASN ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 GLN E 150 GLN H 150 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 23056 Z= 0.298 Angle : 0.577 7.349 30984 Z= 0.304 Chirality : 0.046 0.160 3380 Planarity : 0.003 0.044 3952 Dihedral : 4.134 17.679 3000 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.56 % Favored : 94.30 % Rotamer: Outliers : 1.84 % Allowed : 8.88 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2752 helix: 1.32 (0.16), residues: 1180 sheet: -1.59 (0.26), residues: 436 loop : -1.11 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 126 HIS 0.004 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 *********************** 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 360 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 314 time to evaluate : 2.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 GLU cc_start: 0.7569 (tt0) cc_final: 0.7229 (tt0) REVERT: G 205 GLU cc_start: 0.6642 (pm20) cc_final: 0.5949 (mm-30) REVERT: C 407 GLU cc_start: 0.7561 (tt0) cc_final: 0.7221 (tt0) REVERT: F 78 GLU cc_start: 0.7252 (tm-30) cc_final: 0.7014 (tm-30) REVERT: F 161 ILE cc_start: 0.8024 (mt) cc_final: 0.7817 (mt) REVERT: D 407 GLU cc_start: 0.7486 (tt0) cc_final: 0.7159 (tt0) REVERT: B 407 GLU cc_start: 0.7528 (tt0) cc_final: 0.7210 (tt0) REVERT: E 149 ARG cc_start: 0.8319 (mtm180) cc_final: 0.7978 (mtm180) REVERT: E 205 GLU cc_start: 0.6543 (pm20) cc_final: 0.6113 (mm-30) REVERT: H 205 GLU cc_start: 0.6690 (pm20) cc_final: 0.6067 (mm-30) outliers start: 46 outliers final: 32 residues processed: 350 average time/residue: 0.3104 time to fit residues: 172.1399 Evaluate side-chains 292 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 260 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 554 THR Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 213 ASN 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 294 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain B residue 65 THR 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 501 LEU Chi-restraints excluded: chain B residue 554 THR 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 139 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 208 optimal weight: 0.9990 chunk 170 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 251 optimal weight: 4.9990 chunk 271 optimal weight: 9.9990 chunk 223 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 201 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 GLN G 121 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 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 GLN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 GLN ** 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 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 GLN E 150 GLN E 213 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 23056 Z= 0.416 Angle : 0.628 7.385 30984 Z= 0.338 Chirality : 0.048 0.278 3380 Planarity : 0.004 0.045 3952 Dihedral : 4.478 16.292 3000 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.89 % Favored : 93.97 % Rotamer: Outliers : 2.88 % Allowed : 12.96 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.16), residues: 2752 helix: 0.94 (0.15), residues: 1200 sheet: -1.86 (0.23), residues: 516 loop : -1.52 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 126 HIS 0.007 0.001 HIS E 172 PHE 0.023 0.002 PHE B 28 TYR 0.011 0.002 TYR A 119 ARG 0.005 0.001 ARG B 296 *********************** 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 367 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 295 time to evaluate : 2.719 Fit side-chains revert: symmetry clash REVERT: A 456 LEU cc_start: 0.8020 (mp) cc_final: 0.7624 (mp) REVERT: A 505 ILE cc_start: 0.8196 (mm) cc_final: 0.7921 (mt) REVERT: G 149 ARG cc_start: 0.8396 (mtm180) cc_final: 0.8086 (mtm180) REVERT: C 456 LEU cc_start: 0.7981 (mp) cc_final: 0.7602 (mp) REVERT: C 505 ILE cc_start: 0.8192 (mm) cc_final: 0.7917 (mt) REVERT: F 70 ILE cc_start: 0.8610 (mm) cc_final: 0.8289 (mm) REVERT: F 149 ARG cc_start: 0.8392 (mtm180) cc_final: 0.7930 (mtm180) REVERT: D 456 LEU cc_start: 0.8014 (mp) cc_final: 0.7624 (mp) REVERT: D 505 ILE cc_start: 0.8172 (mm) cc_final: 0.7896 (mt) REVERT: B 456 LEU cc_start: 0.8018 (mp) cc_final: 0.7613 (mp) REVERT: B 505 ILE cc_start: 0.8188 (mm) cc_final: 0.7913 (mt) REVERT: H 70 ILE cc_start: 0.8687 (mm) cc_final: 0.8425 (mm) REVERT: H 149 ARG cc_start: 0.8429 (mtm180) cc_final: 0.7936 (mtm180) outliers start: 72 outliers final: 46 residues processed: 350 average time/residue: 0.3356 time to fit residues: 183.1337 Evaluate side-chains 289 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 243 time to evaluate : 2.771 ------------------------------------------------------------------------------- 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 271 ASN Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain G residue 65 SER 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 343 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 554 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 213 ASN 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 343 VAL Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 554 THR Chi-restraints excluded: chain B residue 42 LEU 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 343 VAL Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 65 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 248 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 168 optimal weight: 0.8980 chunk 251 optimal weight: 0.0570 chunk 266 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 238 optimal weight: 10.0000 chunk 71 optimal weight: 0.5980 overall best weight: 1.0700 ------------------------------------------------------------------------------- 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 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 GLN C 143 ASN ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 GLN C 551 ASN F 213 ASN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 GLN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 GLN B 551 ASN H 150 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3448 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= 0.186 Angle : 0.504 6.811 30984 Z= 0.272 Chirality : 0.043 0.164 3380 Planarity : 0.003 0.043 3952 Dihedral : 4.150 16.146 3000 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.43 % Favored : 95.42 % Rotamer: Outliers : 1.32 % Allowed : 15.64 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.16), residues: 2752 helix: 1.19 (0.16), residues: 1184 sheet: -1.69 (0.24), residues: 472 loop : -1.24 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 126 HIS 0.004 0.001 HIS G 172 PHE 0.021 0.001 PHE F 76 TYR 0.015 0.001 TYR A 278 ARG 0.004 0.000 ARG A 452 *********************** 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 329 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 296 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.7900 (m-80) cc_final: 0.7687 (m-80) REVERT: A 456 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7476 (mp) REVERT: A 505 ILE cc_start: 0.8022 (mm) cc_final: 0.7819 (mt) REVERT: G 149 ARG cc_start: 0.8326 (mtm180) cc_final: 0.8046 (mtm180) REVERT: G 162 ASP cc_start: 0.6770 (m-30) cc_final: 0.6283 (m-30) REVERT: C 456 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7443 (mp) REVERT: F 70 ILE cc_start: 0.8564 (mm) cc_final: 0.8352 (mm) REVERT: F 149 ARG cc_start: 0.8346 (mtm180) cc_final: 0.7920 (mtm180) REVERT: D 456 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7476 (mp) REVERT: B 149 PHE cc_start: 0.7915 (m-80) cc_final: 0.7705 (m-80) REVERT: B 456 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7431 (mp) REVERT: H 70 ILE cc_start: 0.8539 (mm) cc_final: 0.8273 (mm) outliers start: 33 outliers final: 21 residues processed: 319 average time/residue: 0.3517 time to fit residues: 177.0336 Evaluate side-chains 298 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 273 time to evaluate : 2.640 ------------------------------------------------------------------------------- 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 350 ASN Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 350 ASN 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 42 LEU Chi-restraints excluded: chain B residue 271 ASN Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain E residue 32 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 222 optimal weight: 8.9990 chunk 151 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 198 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 227 optimal weight: 0.4980 chunk 184 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 136 optimal weight: 20.0000 chunk 239 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 overall best weight: 3.8988 ------------------------------------------------------------------------------- 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 147 ASN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** 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 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 ASN B 147 ASN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 23056 Z= 0.452 Angle : 0.636 8.726 30984 Z= 0.337 Chirality : 0.047 0.165 3380 Planarity : 0.004 0.048 3952 Dihedral : 4.553 23.740 3000 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.76 % Favored : 93.10 % Rotamer: Outliers : 2.60 % Allowed : 17.48 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.68 (0.16), residues: 2752 helix: 1.03 (0.16), residues: 1168 sheet: -1.83 (0.24), residues: 452 loop : -1.37 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 126 HIS 0.007 0.001 HIS E 172 PHE 0.034 0.002 PHE D 561 TYR 0.016 0.002 TYR D 278 ARG 0.006 0.001 ARG B 296 *********************** 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 342 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 277 time to evaluate : 2.159 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 456 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7497 (mp) REVERT: G 149 ARG cc_start: 0.8420 (mtm180) cc_final: 0.8025 (mtm180) REVERT: C 27 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8882 (tt) REVERT: F 70 ILE cc_start: 0.8696 (mm) cc_final: 0.8495 (mm) REVERT: F 149 ARG cc_start: 0.8410 (mtm180) cc_final: 0.7925 (mtm180) REVERT: D 456 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7508 (mp) REVERT: B 27 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8870 (tt) REVERT: B 42 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8566 (mm) REVERT: E 162 ASP cc_start: 0.6953 (m-30) cc_final: 0.6455 (m-30) REVERT: H 149 ARG cc_start: 0.8429 (mtm180) cc_final: 0.7948 (mtm180) outliers start: 65 outliers final: 44 residues processed: 323 average time/residue: 0.3761 time to fit residues: 186.9653 Evaluate side-chains 301 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 252 time to evaluate : 2.712 ------------------------------------------------------------------------------- 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 343 VAL Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain C residue 27 ILE 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 331 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain D residue 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 343 VAL Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 350 ASN 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 27 ILE Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 271 ASN Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain H residue 65 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 89 optimal weight: 1.9990 chunk 240 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 156 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 267 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 ASN ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 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 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23056 Z= 0.179 Angle : 0.521 9.729 30984 Z= 0.276 Chirality : 0.043 0.177 3380 Planarity : 0.003 0.050 3952 Dihedral : 4.223 18.524 3000 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.14 % Favored : 95.71 % Rotamer: Outliers : 2.56 % Allowed : 17.76 % Favored : 79.68 % 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: -0.46 (0.16), residues: 2752 helix: 1.14 (0.16), residues: 1184 sheet: -1.81 (0.25), residues: 436 loop : -1.16 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 126 HIS 0.004 0.001 HIS F 172 PHE 0.026 0.001 PHE D 561 TYR 0.014 0.001 TYR E 126 ARG 0.004 0.000 ARG E 83 *********************** 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 357 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 293 time to evaluate : 2.647 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: symmetry clash REVERT: A 149 PHE cc_start: 0.7888 (m-80) cc_final: 0.7649 (m-80) REVERT: G 149 ARG cc_start: 0.8320 (mtm180) cc_final: 0.8010 (mtm180) REVERT: G 161 ILE cc_start: 0.8282 (mt) cc_final: 0.8080 (mt) REVERT: F 70 ILE cc_start: 0.8730 (mm) cc_final: 0.8516 (mm) REVERT: F 149 ARG cc_start: 0.8342 (mtm180) cc_final: 0.7891 (mtm180) REVERT: B 149 PHE cc_start: 0.7931 (m-80) cc_final: 0.7693 (m-80) REVERT: H 149 ARG cc_start: 0.8354 (mtm180) cc_final: 0.7916 (mtm180) outliers start: 64 outliers final: 46 residues processed: 339 average time/residue: 0.3567 time to fit residues: 188.4032 Evaluate side-chains 325 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 279 time to evaluate : 2.584 ------------------------------------------------------------------------------- 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 134 ILE Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 350 ASN 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 42 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 271 ASN Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 350 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 32 GLU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain H residue 65 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 257 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 224 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 266 optimal weight: 0.0170 chunk 166 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 ASN ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 ASN ** 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 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23056 Z= 0.263 Angle : 0.537 6.336 30984 Z= 0.287 Chirality : 0.044 0.167 3380 Planarity : 0.003 0.053 3952 Dihedral : 4.223 19.260 3000 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.92 % Favored : 93.93 % Rotamer: Outliers : 2.56 % Allowed : 17.52 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.37 (0.17), residues: 2752 helix: 1.17 (0.16), residues: 1180 sheet: -1.77 (0.25), residues: 420 loop : -1.09 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 126 HIS 0.005 0.001 HIS F 172 PHE 0.023 0.002 PHE D 561 TYR 0.010 0.001 TYR B 278 ARG 0.003 0.000 ARG E 83 *********************** 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 359 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 295 time to evaluate : 2.587 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: symmetry clash revert: symmetry clash REVERT: G 149 ARG cc_start: 0.8321 (mtm180) cc_final: 0.8003 (mtm180) REVERT: G 161 ILE cc_start: 0.8310 (mt) cc_final: 0.8074 (mt) REVERT: C 27 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8776 (tt) REVERT: F 149 ARG cc_start: 0.8392 (mtm180) cc_final: 0.7908 (mtm180) REVERT: B 27 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8789 (tt) REVERT: H 149 ARG cc_start: 0.8410 (mtm180) cc_final: 0.7922 (mtm180) outliers start: 64 outliers final: 50 residues processed: 342 average time/residue: 0.3550 time to fit residues: 188.0629 Evaluate side-chains 328 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 276 time to evaluate : 2.528 ------------------------------------------------------------------------------- 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 134 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 271 ASN Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 350 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 65 SER Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 88 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 164 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 209 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 ASN ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 ASN ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 ASN ** 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 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 23056 Z= 0.440 Angle : 0.639 7.620 30984 Z= 0.339 Chirality : 0.048 0.168 3380 Planarity : 0.004 0.053 3952 Dihedral : 4.592 21.272 3000 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.94 % Favored : 92.91 % Rotamer: Outliers : 2.76 % Allowed : 18.08 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.16), residues: 2752 helix: 0.99 (0.16), residues: 1168 sheet: -1.94 (0.24), residues: 456 loop : -1.32 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 126 HIS 0.007 0.001 HIS F 172 PHE 0.022 0.002 PHE A 561 TYR 0.013 0.002 TYR A 493 ARG 0.005 0.001 ARG C 332 *********************** 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 fitting. rotamer outliers: 69 poor density : 263 time to evaluate : 2.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8816 (tt) REVERT: G 146 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.7861 (pt) REVERT: G 149 ARG cc_start: 0.8423 (mtm180) cc_final: 0.8093 (mtm180) REVERT: G 161 ILE cc_start: 0.8373 (mt) cc_final: 0.8148 (mt) REVERT: C 27 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8890 (tt) REVERT: F 149 ARG cc_start: 0.8428 (mtm180) cc_final: 0.7882 (mtm180) REVERT: F 161 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7965 (mt) REVERT: D 27 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8821 (tt) REVERT: B 27 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8883 (tt) outliers start: 69 outliers final: 49 residues processed: 313 average time/residue: 0.3444 time to fit residues: 166.9578 Evaluate side-chains 314 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 259 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 40 TYR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 271 ASN Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 350 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 65 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 88 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.272 > 50: distance: 32 - 179: 9.247 distance: 35 - 176: 11.107 distance: 45 - 163: 5.215 distance: 48 - 160: 11.985 distance: 122 - 126: 11.507 distance: 126 - 127: 11.014 distance: 127 - 128: 21.210 distance: 127 - 130: 8.608 distance: 128 - 129: 16.895 distance: 128 - 135: 47.283 distance: 130 - 131: 18.561 distance: 131 - 132: 17.619 distance: 132 - 133: 5.975 distance: 133 - 134: 15.094 distance: 135 - 136: 9.379 distance: 135 - 297: 30.920 distance: 136 - 137: 22.122 distance: 136 - 139: 10.345 distance: 137 - 138: 19.319 distance: 137 - 143: 19.326 distance: 138 - 294: 12.400 distance: 139 - 140: 13.775 distance: 139 - 141: 8.490 distance: 140 - 142: 27.585 distance: 143 - 144: 17.628 distance: 144 - 147: 14.264 distance: 145 - 146: 8.274 distance: 145 - 152: 15.229 distance: 147 - 148: 5.254 distance: 148 - 149: 7.664 distance: 149 - 150: 4.029 distance: 149 - 151: 21.411 distance: 152 - 153: 10.924 distance: 153 - 154: 18.019 distance: 154 - 155: 24.934 distance: 154 - 160: 11.002 distance: 156 - 157: 3.726 distance: 156 - 158: 11.476 distance: 157 - 159: 11.456 distance: 160 - 161: 11.237 distance: 161 - 162: 14.078 distance: 161 - 164: 5.559 distance: 162 - 163: 10.929 distance: 162 - 168: 11.743 distance: 164 - 165: 12.789 distance: 164 - 166: 7.703 distance: 165 - 167: 12.555 distance: 168 - 169: 7.287 distance: 168 - 268: 6.145 distance: 169 - 170: 7.170 distance: 170 - 171: 3.867 distance: 170 - 176: 4.776 distance: 171 - 265: 11.209 distance: 172 - 173: 5.689 distance: 173 - 174: 5.711 distance: 176 - 177: 10.722 distance: 177 - 178: 5.898 distance: 177 - 180: 4.865 distance: 178 - 179: 7.151 distance: 178 - 183: 8.056 distance: 180 - 181: 13.284 distance: 180 - 182: 11.793 distance: 183 - 184: 3.709 distance: 183 - 250: 11.619 distance: 184 - 185: 4.701 distance: 184 - 187: 8.531 distance: 185 - 186: 16.093 distance: 185 - 191: 3.951 distance: 186 - 247: 19.148 distance: 187 - 188: 4.894 distance: 188 - 189: 10.151 distance: 191 - 192: 6.268 distance: 192 - 193: 14.101 distance: 192 - 195: 6.841 distance: 193 - 194: 6.626 distance: 193 - 199: 17.326 distance: 195 - 196: 13.626 distance: 196 - 197: 27.677 distance: 196 - 198: 21.172 distance: 199 - 200: 11.535 distance: 200 - 201: 3.427 distance: 200 - 203: 12.417 distance: 201 - 202: 14.366 distance: 201 - 207: 4.450 distance: 203 - 204: 13.196 distance: 204 - 206: 8.249