Starting phenix.real_space_refine on Thu Mar 5 06:18:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dkj_30707/03_2026/7dkj_30707.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dkj_30707/03_2026/7dkj_30707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dkj_30707/03_2026/7dkj_30707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dkj_30707/03_2026/7dkj_30707.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dkj_30707/03_2026/7dkj_30707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dkj_30707/03_2026/7dkj_30707.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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 114 5.16 5 C 12633 2.51 5 N 3381 2.21 5 O 3984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20112 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3947 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 19, 'TRANS': 478} Chain: "C" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1381 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 165} Chain: "D" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "E" Number of atoms: 3947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3947 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 19, 'TRANS': 478} Chain: "G" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1381 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 165} Chain: "H" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "I" Number of atoms: 3947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3947 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 19, 'TRANS': 478} Chain: "K" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1381 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 165} Chain: "L" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.18, per 1000 atoms: 0.21 Number of scatterers: 20112 At special positions: 0 Unit cell: (154.35, 149.94, 148.47, 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 114 16.00 O 3984 8.00 N 3381 7.00 C 12633 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 464 " distance=2.03 Simple disulfide: pdb=" SG CYS A 44 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 69 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 303 " distance=2.02 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 98 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS D 147 " distance=1.92 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 464 " distance=2.03 Simple disulfide: pdb=" SG CYS E 44 " - pdb=" SG CYS E 275 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 69 " distance=2.03 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 279 " - pdb=" SG CYS E 303 " distance=2.02 Simple disulfide: pdb=" SG CYS E 471 " - pdb=" SG CYS E 475 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 98 " distance=2.03 Simple disulfide: pdb=" SG CYS G 121 " - pdb=" SG CYS H 147 " distance=1.97 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 6 " - pdb=" SG CYS I 464 " distance=2.03 Simple disulfide: pdb=" SG CYS I 44 " - pdb=" SG CYS I 275 " distance=2.03 Simple disulfide: pdb=" SG CYS I 57 " - pdb=" SG CYS I 69 " distance=2.03 Simple disulfide: pdb=" SG CYS I 92 " - pdb=" SG CYS I 136 " distance=2.03 Simple disulfide: pdb=" SG CYS I 279 " - pdb=" SG CYS I 303 " distance=2.02 Simple disulfide: pdb=" SG CYS I 471 " - pdb=" SG CYS I 475 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 98 " distance=2.03 Simple disulfide: pdb=" SG CYS K 121 " - pdb=" SG CYS L 147 " distance=2.21 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 601 " - " ASN A 13 " " NAG A 602 " - " ASN A 25 " " NAG A 603 " - " ASN A 287 " " NAG B 1 " - " ASN A 166 " " NAG E 601 " - " ASN E 13 " " NAG E 602 " - " ASN E 25 " " NAG E 603 " - " ASN E 287 " " NAG F 1 " - " ASN A 481 " " NAG I 601 " - " ASN I 13 " " NAG I 602 " - " ASN I 25 " " NAG I 603 " - " ASN I 287 " " NAG J 1 " - " ASN E 166 " " NAG M 1 " - " ASN E 481 " " NAG N 1 " - " ASN I 166 " " NAG O 1 " - " ASN I 481 " Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 773.8 milliseconds 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4560 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 45 sheets defined 28.1% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 58 through 65 Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 184 through 193 Processing helix chain 'A' and resid 364 through 386 Processing helix chain 'A' and resid 398 through 400 No H-bonds generated for 'chain 'A' and resid 398 through 400' Processing helix chain 'A' and resid 401 through 453 removed outlier: 3.938A pdb=" N LEU A 426 " --> pdb=" O ASN A 422 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 481 Processing helix chain 'A' and resid 485 through 499 removed outlier: 3.825A pdb=" N TYR A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU A 491 " --> pdb=" O PRO A 487 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLU A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 57 removed outlier: 3.841A pdb=" N ASN C 56 " --> pdb=" O ASP C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 67 Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 133 through 170 Proline residue: C 146 - end of helix Proline residue: C 165 - end of helix Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 120 through 159 removed outlier: 3.806A pdb=" N GLN D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASP D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Proline residue: D 132 - end of helix Proline residue: D 151 - end of helix removed outlier: 3.715A pdb=" N LYS D 159 " --> pdb=" O ALA D 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 65 Processing helix chain 'E' and resid 99 through 108 Processing helix chain 'E' and resid 184 through 193 Processing helix chain 'E' and resid 364 through 386 Processing helix chain 'E' and resid 398 through 400 No H-bonds generated for 'chain 'E' and resid 398 through 400' Processing helix chain 'E' and resid 401 through 453 removed outlier: 3.939A pdb=" N LEU E 426 " --> pdb=" O ASN E 422 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE E 437 " --> pdb=" O ARG E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 481 Processing helix chain 'E' and resid 485 through 499 removed outlier: 3.824A pdb=" N TYR E 489 " --> pdb=" O ASP E 485 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU E 491 " --> pdb=" O PRO E 487 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLU E 492 " --> pdb=" O LYS E 488 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU E 499 " --> pdb=" O LEU E 495 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 57 removed outlier: 3.842A pdb=" N ASN G 56 " --> pdb=" O ASP G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 67 Processing helix chain 'G' and resid 76 through 78 No H-bonds generated for 'chain 'G' and resid 76 through 78' Processing helix chain 'G' and resid 89 through 93 Processing helix chain 'G' and resid 133 through 170 Proline residue: G 146 - end of helix Proline residue: G 165 - end of helix Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'H' and resid 120 through 159 removed outlier: 3.806A pdb=" N GLN H 124 " --> pdb=" O VAL H 120 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASP H 131 " --> pdb=" O LEU H 127 " (cutoff:3.500A) Proline residue: H 132 - end of helix Proline residue: H 151 - end of helix removed outlier: 3.715A pdb=" N LYS H 159 " --> pdb=" O ALA H 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 65 Processing helix chain 'I' and resid 99 through 108 Processing helix chain 'I' and resid 184 through 193 Processing helix chain 'I' and resid 364 through 386 Processing helix chain 'I' and resid 398 through 400 No H-bonds generated for 'chain 'I' and resid 398 through 400' Processing helix chain 'I' and resid 401 through 453 removed outlier: 3.938A pdb=" N LEU I 426 " --> pdb=" O ASN I 422 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE I 437 " --> pdb=" O ARG I 433 " (cutoff:3.500A) Processing helix chain 'I' and resid 472 through 481 Processing helix chain 'I' and resid 485 through 499 removed outlier: 3.825A pdb=" N TYR I 489 " --> pdb=" O ASP I 485 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU I 491 " --> pdb=" O PRO I 487 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLU I 492 " --> pdb=" O LYS I 488 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU I 499 " --> pdb=" O LEU I 495 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 57 removed outlier: 3.841A pdb=" N ASN K 56 " --> pdb=" O ASP K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 67 Processing helix chain 'K' and resid 76 through 78 No H-bonds generated for 'chain 'K' and resid 76 through 78' Processing helix chain 'K' and resid 89 through 93 Processing helix chain 'K' and resid 133 through 170 Proline residue: K 146 - end of helix Proline residue: K 165 - end of helix Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 120 through 159 removed outlier: 3.806A pdb=" N GLN L 124 " --> pdb=" O VAL L 120 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASP L 131 " --> pdb=" O LEU L 127 " (cutoff:3.500A) Proline residue: L 132 - end of helix Proline residue: L 151 - end of helix removed outlier: 3.715A pdb=" N LYS L 159 " --> pdb=" O ALA L 155 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 9 Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 18 Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 33 Processing sheet with id=AA4, first strand: chain 'A' and resid 44 through 46 removed outlier: 6.599A pdb=" N LYS A 45 " --> pdb=" O THR A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 83 removed outlier: 6.817A pdb=" N ILE A 81 " --> pdb=" O ILE A 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 112 through 117 removed outlier: 6.737A pdb=" N HIS A 112 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR A 253 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE A 176 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE A 176 " --> pdb=" O PRO A 251 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 112 through 117 removed outlier: 6.737A pdb=" N HIS A 112 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR A 253 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE A 176 " --> pdb=" O TYR A 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 161 through 165 Processing sheet with id=AA9, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AB1, first strand: chain 'A' and resid 457 through 458 Processing sheet with id=AB2, first strand: chain 'C' and resid 4 through 7 removed outlier: 4.026A pdb=" N ILE C 80 " --> pdb=" O ASP C 75 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.608A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET C 34 " --> pdb=" O PHE C 50 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N CYS C 98 " --> pdb=" O TRP C 112 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TRP C 112 " --> pdb=" O CYS C 98 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG C 100 " --> pdb=" O ASP C 110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.608A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET C 34 " --> pdb=" O PHE C 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'E' and resid 5 through 9 Processing sheet with id=AB8, first strand: chain 'E' and resid 17 through 18 Processing sheet with id=AB9, first strand: chain 'E' and resid 32 through 33 Processing sheet with id=AC1, first strand: chain 'E' and resid 44 through 46 removed outlier: 6.599A pdb=" N LYS E 45 " --> pdb=" O THR E 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 81 through 83 removed outlier: 6.819A pdb=" N ILE E 81 " --> pdb=" O ILE E 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 112 through 117 removed outlier: 6.738A pdb=" N HIS E 112 " --> pdb=" O SER E 258 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR E 253 " --> pdb=" O ILE E 176 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE E 176 " --> pdb=" O TYR E 253 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE E 176 " --> pdb=" O PRO E 251 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 112 through 117 removed outlier: 6.738A pdb=" N HIS E 112 " --> pdb=" O SER E 258 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR E 253 " --> pdb=" O ILE E 176 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE E 176 " --> pdb=" O TYR E 253 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 161 through 165 Processing sheet with id=AC6, first strand: chain 'E' and resid 292 through 293 Processing sheet with id=AC7, first strand: chain 'E' and resid 457 through 458 Processing sheet with id=AC8, first strand: chain 'G' and resid 4 through 7 removed outlier: 4.025A pdb=" N ILE G 80 " --> pdb=" O ASP G 75 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 46 through 51 removed outlier: 6.609A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N MET G 34 " --> pdb=" O PHE G 50 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N CYS G 98 " --> pdb=" O TRP G 112 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TRP G 112 " --> pdb=" O CYS G 98 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG G 100 " --> pdb=" O ASP G 110 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 46 through 51 removed outlier: 6.609A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N MET G 34 " --> pdb=" O PHE G 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 19 through 24 Processing sheet with id=AD3, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AD4, first strand: chain 'I' and resid 5 through 9 Processing sheet with id=AD5, first strand: chain 'I' and resid 17 through 18 Processing sheet with id=AD6, first strand: chain 'I' and resid 32 through 33 Processing sheet with id=AD7, first strand: chain 'I' and resid 44 through 46 removed outlier: 6.599A pdb=" N LYS I 45 " --> pdb=" O THR I 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'I' and resid 81 through 83 removed outlier: 6.818A pdb=" N ILE I 81 " --> pdb=" O ILE I 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'I' and resid 112 through 117 removed outlier: 6.738A pdb=" N HIS I 112 " --> pdb=" O SER I 258 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR I 253 " --> pdb=" O ILE I 176 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE I 176 " --> pdb=" O TYR I 253 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE I 176 " --> pdb=" O PRO I 251 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 112 through 117 removed outlier: 6.738A pdb=" N HIS I 112 " --> pdb=" O SER I 258 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR I 253 " --> pdb=" O ILE I 176 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE I 176 " --> pdb=" O TYR I 253 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 161 through 165 Processing sheet with id=AE3, first strand: chain 'I' and resid 292 through 293 Processing sheet with id=AE4, first strand: chain 'I' and resid 457 through 458 Processing sheet with id=AE5, first strand: chain 'K' and resid 4 through 7 removed outlier: 4.025A pdb=" N ILE K 80 " --> pdb=" O ASP K 75 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 46 through 51 removed outlier: 6.608A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET K 34 " --> pdb=" O PHE K 50 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N CYS K 98 " --> pdb=" O TRP K 112 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TRP K 112 " --> pdb=" O CYS K 98 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG K 100 " --> pdb=" O ASP K 110 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 46 through 51 removed outlier: 6.608A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET K 34 " --> pdb=" O PHE K 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AE9, first strand: chain 'L' and resid 53 through 54 822 hydrogen bonds defined for protein. 2232 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: 2.90 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6501 1.34 - 1.46: 4648 1.46 - 1.58: 9233 1.58 - 1.70: 0 1.70 - 1.82: 168 Bond restraints: 20550 Sorted by residual: bond pdb=" C1 BMA O 3 " pdb=" C2 BMA O 3 " ideal model delta sigma weight residual 1.519 1.571 -0.052 2.00e-02 2.50e+03 6.72e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.571 -0.052 2.00e-02 2.50e+03 6.63e+00 bond pdb=" C1 BMA M 3 " pdb=" C2 BMA M 3 " ideal model delta sigma weight residual 1.519 1.570 -0.051 2.00e-02 2.50e+03 6.62e+00 bond pdb=" CG1 ILE A 383 " pdb=" CD1 ILE A 383 " ideal model delta sigma weight residual 1.513 1.415 0.098 3.90e-02 6.57e+02 6.29e+00 bond pdb=" CG1 ILE E 383 " pdb=" CD1 ILE E 383 " ideal model delta sigma weight residual 1.513 1.415 0.098 3.90e-02 6.57e+02 6.25e+00 ... (remaining 20545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 26860 2.09 - 4.18: 780 4.18 - 6.26: 105 6.26 - 8.35: 38 8.35 - 10.44: 12 Bond angle restraints: 27795 Sorted by residual: angle pdb=" CA GLN K 78 " pdb=" CB GLN K 78 " pdb=" CG GLN K 78 " ideal model delta sigma weight residual 114.10 124.54 -10.44 2.00e+00 2.50e-01 2.72e+01 angle pdb=" CA GLN C 78 " pdb=" CB GLN C 78 " pdb=" CG GLN C 78 " ideal model delta sigma weight residual 114.10 124.53 -10.43 2.00e+00 2.50e-01 2.72e+01 angle pdb=" CA GLN G 78 " pdb=" CB GLN G 78 " pdb=" CG GLN G 78 " ideal model delta sigma weight residual 114.10 124.52 -10.42 2.00e+00 2.50e-01 2.71e+01 angle pdb=" CB GLN C 78 " pdb=" CG GLN C 78 " pdb=" CD GLN C 78 " ideal model delta sigma weight residual 112.60 118.99 -6.39 1.70e+00 3.46e-01 1.41e+01 angle pdb=" CB GLN K 78 " pdb=" CG GLN K 78 " pdb=" CD GLN K 78 " ideal model delta sigma weight residual 112.60 118.99 -6.39 1.70e+00 3.46e-01 1.41e+01 ... (remaining 27790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.28: 11331 21.28 - 42.56: 955 42.56 - 63.84: 172 63.84 - 85.11: 119 85.11 - 106.39: 104 Dihedral angle restraints: 12681 sinusoidal: 5529 harmonic: 7152 Sorted by residual: dihedral pdb=" CB CYS E 44 " pdb=" SG CYS E 44 " pdb=" SG CYS E 275 " pdb=" CB CYS E 275 " ideal model delta sinusoidal sigma weight residual -86.00 -9.61 -76.39 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CB CYS I 44 " pdb=" SG CYS I 44 " pdb=" SG CYS I 275 " pdb=" CB CYS I 275 " ideal model delta sinusoidal sigma weight residual -86.00 -9.62 -76.38 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CB CYS A 44 " pdb=" SG CYS A 44 " pdb=" SG CYS A 275 " pdb=" CB CYS A 275 " ideal model delta sinusoidal sigma weight residual -86.00 -9.64 -76.36 1 1.00e+01 1.00e-02 7.34e+01 ... (remaining 12678 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2846 0.097 - 0.194: 190 0.194 - 0.291: 9 0.291 - 0.387: 0 0.387 - 0.484: 3 Chirality restraints: 3048 Sorted by residual: chirality pdb=" C1 NAG I 602 " pdb=" ND2 ASN I 25 " pdb=" C2 NAG I 602 " pdb=" O5 NAG I 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.87e+00 chirality pdb=" C1 NAG E 602 " pdb=" ND2 ASN E 25 " pdb=" C2 NAG E 602 " pdb=" O5 NAG E 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.79e+00 chirality pdb=" C1 NAG A 602 " pdb=" ND2 ASN A 25 " pdb=" C2 NAG A 602 " pdb=" O5 NAG A 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.78e+00 ... (remaining 3045 not shown) Planarity restraints: 3582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 94 " -0.047 5.00e-02 4.00e+02 7.16e-02 8.19e+00 pdb=" N PRO D 95 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 95 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 95 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR L 94 " -0.047 5.00e-02 4.00e+02 7.14e-02 8.15e+00 pdb=" N PRO L 95 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR H 94 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.12e+00 pdb=" N PRO H 95 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO H 95 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO H 95 " 0.040 5.00e-02 4.00e+02 ... (remaining 3579 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 348 2.62 - 3.19: 19418 3.19 - 3.76: 31253 3.76 - 4.33: 43362 4.33 - 4.90: 71032 Nonbonded interactions: 165413 Sorted by model distance: nonbonded pdb=" OG1 THR E 128 " pdb=" OG1 THR E 152 " model vdw 2.056 3.040 nonbonded pdb=" OG1 THR A 128 " pdb=" OG1 THR A 152 " model vdw 2.056 3.040 nonbonded pdb=" OG1 THR I 128 " pdb=" OG1 THR I 152 " model vdw 2.056 3.040 nonbonded pdb=" NZ LYS L 39 " pdb=" O GLU L 81 " model vdw 2.090 3.120 nonbonded pdb=" NZ LYS D 39 " pdb=" O GLU D 81 " model vdw 2.090 3.120 ... (remaining 165408 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } 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: 0.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.490 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 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 : 0.008 0.182 20604 Z= 0.338 Angle : 0.896 11.412 27930 Z= 0.468 Chirality : 0.054 0.484 3048 Planarity : 0.005 0.072 3567 Dihedral : 20.249 106.392 8040 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 1.84 % Allowed : 2.26 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.16), residues: 2472 helix: -1.01 (0.20), residues: 597 sheet: -1.31 (0.22), residues: 567 loop : -1.91 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG K 54 TYR 0.023 0.002 TYR L 145 PHE 0.015 0.002 PHE I 229 TRP 0.032 0.002 TRP I 150 HIS 0.005 0.001 HIS I 10 Details of bonding type rmsd covalent geometry : bond 0.00745 (20550) covalent geometry : angle 0.87271 (27795) SS BOND : bond 0.04307 ( 27) SS BOND : angle 1.99002 ( 54) hydrogen bonds : bond 0.16516 ( 774) hydrogen bonds : angle 8.30846 ( 2232) link_BETA1-4 : bond 0.01318 ( 12) link_BETA1-4 : angle 3.17871 ( 36) link_NAG-ASN : bond 0.00350 ( 15) link_NAG-ASN : angle 3.90330 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 418 time to evaluate : 0.727 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7848 (tp) REVERT: A 337 ILE cc_start: 0.8898 (mm) cc_final: 0.8591 (mm) REVERT: A 411 MET cc_start: 0.8349 (tmm) cc_final: 0.7653 (tmm) REVERT: A 412 GLU cc_start: 0.7140 (tt0) cc_final: 0.6598 (tt0) REVERT: A 433 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.5783 (mmt-90) REVERT: A 451 MET cc_start: 0.8506 (ttm) cc_final: 0.8280 (ttm) REVERT: C 78 GLN cc_start: 0.5983 (OUTLIER) cc_final: 0.4934 (pt0) REVERT: C 96 TYR cc_start: 0.7132 (m-80) cc_final: 0.6758 (m-80) REVERT: C 109 MET cc_start: 0.8181 (mmm) cc_final: 0.7926 (mmm) REVERT: D 145 TYR cc_start: 0.4520 (OUTLIER) cc_final: 0.3807 (m-10) REVERT: E 21 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8198 (tp) REVERT: E 93 PHE cc_start: 0.7461 (t80) cc_final: 0.7185 (t80) REVERT: E 175 ILE cc_start: 0.9200 (mm) cc_final: 0.8904 (mm) REVERT: E 236 MET cc_start: 0.6893 (OUTLIER) cc_final: 0.6507 (mmp) REVERT: E 260 ARG cc_start: 0.7827 (mmm160) cc_final: 0.7511 (mmp80) REVERT: E 271 THR cc_start: 0.8401 (t) cc_final: 0.8098 (m) REVERT: E 308 LYS cc_start: 0.8300 (mtpp) cc_final: 0.7951 (mttm) REVERT: E 324 ILE cc_start: 0.6598 (OUTLIER) cc_final: 0.6381 (pt) REVERT: E 337 ILE cc_start: 0.9031 (mm) cc_final: 0.8701 (mm) REVERT: E 341 TRP cc_start: 0.8748 (m-10) cc_final: 0.8383 (m-10) REVERT: E 411 MET cc_start: 0.8436 (tmm) cc_final: 0.7977 (tmm) REVERT: E 412 GLU cc_start: 0.7038 (tt0) cc_final: 0.6689 (mt-10) REVERT: E 468 TYR cc_start: 0.7936 (m-80) cc_final: 0.7404 (m-80) REVERT: G 12 VAL cc_start: 0.8499 (t) cc_final: 0.8078 (m) REVERT: G 31 ASP cc_start: 0.7817 (p0) cc_final: 0.7576 (p0) REVERT: G 33 TYR cc_start: 0.7753 (m-80) cc_final: 0.7549 (m-10) REVERT: G 34 MET cc_start: 0.6892 (tpp) cc_final: 0.6675 (tpt) REVERT: G 35 THR cc_start: 0.7670 (m) cc_final: 0.7402 (m) REVERT: G 71 THR cc_start: 0.7846 (p) cc_final: 0.7620 (p) REVERT: G 73 SER cc_start: 0.7804 (OUTLIER) cc_final: 0.7499 (m) REVERT: G 78 GLN cc_start: 0.5270 (OUTLIER) cc_final: 0.4974 (mp10) REVERT: G 109 MET cc_start: 0.7563 (mmm) cc_final: 0.7233 (mmm) REVERT: H 145 TYR cc_start: 0.4181 (OUTLIER) cc_final: 0.3332 (m-80) REVERT: I 83 GLU cc_start: 0.7409 (tt0) cc_final: 0.6882 (tt0) REVERT: I 93 PHE cc_start: 0.7395 (t80) cc_final: 0.7133 (t80) REVERT: I 146 ARG cc_start: 0.6687 (mpt180) cc_final: 0.6477 (mmt-90) REVERT: I 236 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6998 (mmp) REVERT: I 308 LYS cc_start: 0.8542 (mtpp) cc_final: 0.8271 (mttp) REVERT: I 324 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7451 (pt) REVERT: I 355 ASN cc_start: 0.8739 (t0) cc_final: 0.8458 (t0) REVERT: I 468 TYR cc_start: 0.8669 (m-80) cc_final: 0.8448 (m-80) REVERT: K 12 VAL cc_start: 0.7479 (t) cc_final: 0.7190 (m) REVERT: K 13 GLN cc_start: 0.7329 (mm110) cc_final: 0.7092 (mm110) REVERT: K 73 SER cc_start: 0.7557 (OUTLIER) cc_final: 0.7345 (m) REVERT: K 109 MET cc_start: 0.7504 (mmm) cc_final: 0.7156 (mmm) REVERT: K 149 GLU cc_start: 0.4278 (mp0) cc_final: 0.3895 (mm-30) REVERT: L 145 TYR cc_start: 0.4942 (OUTLIER) cc_final: 0.3674 (m-80) outliers start: 40 outliers final: 7 residues processed: 444 average time/residue: 0.1418 time to fit residues: 96.8749 Evaluate side-chains 342 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 321 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain C residue 78 GLN Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 145 TYR Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 78 GLN Chi-restraints excluded: chain H residue 145 TYR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 236 MET Chi-restraints excluded: chain I residue 324 ILE Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain L residue 145 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 9.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 353 HIS A 477 ASN C 13 GLN C 157 GLN D 6 GLN ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN E 353 HIS E 377 ASN E 408 ASN E 477 ASN G 157 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN H 146 GLN ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN I 377 ASN I 477 ASN K 157 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.190687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.183506 restraints weight = 25430.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.169066 restraints weight = 44444.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.165145 restraints weight = 58489.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.163894 restraints weight = 58308.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.164227 restraints weight = 43730.075| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20604 Z= 0.173 Angle : 0.763 10.918 27930 Z= 0.382 Chirality : 0.049 0.403 3048 Planarity : 0.005 0.056 3567 Dihedral : 14.554 81.728 3304 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.07 % Allowed : 10.79 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.16), residues: 2472 helix: 0.68 (0.22), residues: 591 sheet: -1.25 (0.22), residues: 534 loop : -1.76 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 260 TYR 0.022 0.002 TYR K 62 PHE 0.012 0.002 PHE I 372 TRP 0.023 0.002 TRP E 150 HIS 0.013 0.002 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00387 (20550) covalent geometry : angle 0.73449 (27795) SS BOND : bond 0.00591 ( 27) SS BOND : angle 2.18043 ( 54) hydrogen bonds : bond 0.05158 ( 774) hydrogen bonds : angle 5.74680 ( 2232) link_BETA1-4 : bond 0.01585 ( 12) link_BETA1-4 : angle 3.77284 ( 36) link_NAG-ASN : bond 0.00643 ( 15) link_NAG-ASN : angle 3.38882 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 333 time to evaluate : 0.640 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: A 21 ILE cc_start: 0.8031 (mm) cc_final: 0.7745 (tp) REVERT: A 36 GLU cc_start: 0.7114 (tp30) cc_final: 0.6870 (tp30) REVERT: A 337 ILE cc_start: 0.8948 (mm) cc_final: 0.8544 (mm) REVERT: A 411 MET cc_start: 0.8928 (tmm) cc_final: 0.8407 (tmm) REVERT: A 412 GLU cc_start: 0.7190 (tt0) cc_final: 0.6538 (mt-10) REVERT: A 433 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6085 (mtt-85) REVERT: C 60 THR cc_start: 0.8298 (m) cc_final: 0.7770 (p) REVERT: C 78 GLN cc_start: 0.6388 (mp10) cc_final: 0.5671 (pt0) REVERT: C 109 MET cc_start: 0.8092 (mmm) cc_final: 0.7826 (mmm) REVERT: C 144 LEU cc_start: 0.4782 (tt) cc_final: 0.4470 (mp) REVERT: E 115 LYS cc_start: 0.7358 (ttmt) cc_final: 0.6775 (ttmt) REVERT: E 271 THR cc_start: 0.8432 (t) cc_final: 0.8107 (m) REVERT: E 308 LYS cc_start: 0.8466 (mtpp) cc_final: 0.8135 (mttm) REVERT: E 324 ILE cc_start: 0.6457 (OUTLIER) cc_final: 0.6237 (pt) REVERT: E 337 ILE cc_start: 0.9060 (mm) cc_final: 0.8725 (mm) REVERT: E 341 TRP cc_start: 0.8682 (m-10) cc_final: 0.7453 (m-10) REVERT: E 411 MET cc_start: 0.8868 (tmm) cc_final: 0.8492 (tmm) REVERT: E 412 GLU cc_start: 0.7026 (tt0) cc_final: 0.6783 (mt-10) REVERT: E 433 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6579 (mmp80) REVERT: E 466 GLU cc_start: 0.7894 (tt0) cc_final: 0.7549 (tt0) REVERT: E 468 TYR cc_start: 0.7875 (m-80) cc_final: 0.7520 (m-80) REVERT: G 12 VAL cc_start: 0.8462 (t) cc_final: 0.8001 (m) REVERT: G 31 ASP cc_start: 0.7744 (p0) cc_final: 0.7416 (p0) REVERT: G 70 PHE cc_start: 0.7489 (m-10) cc_final: 0.7275 (m-10) REVERT: G 109 MET cc_start: 0.7752 (mmm) cc_final: 0.7477 (mmm) REVERT: G 149 GLU cc_start: 0.2250 (mp0) cc_final: 0.1822 (mm-30) REVERT: H 133 MET cc_start: 0.1533 (ppp) cc_final: 0.0465 (tpt) REVERT: I 83 GLU cc_start: 0.7303 (tt0) cc_final: 0.6895 (tt0) REVERT: I 115 LYS cc_start: 0.8276 (ttpp) cc_final: 0.7813 (ttmm) REVERT: I 217 ARG cc_start: 0.7207 (mtt90) cc_final: 0.6813 (mtt90) REVERT: I 308 LYS cc_start: 0.8582 (mtpp) cc_final: 0.8382 (mttp) REVERT: I 324 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7492 (pt) REVERT: I 337 ILE cc_start: 0.9128 (mm) cc_final: 0.8771 (mm) REVERT: I 433 ARG cc_start: 0.6905 (OUTLIER) cc_final: 0.5964 (mmp-170) REVERT: I 466 GLU cc_start: 0.7789 (tt0) cc_final: 0.7426 (tm-30) REVERT: K 13 GLN cc_start: 0.7291 (mm110) cc_final: 0.7066 (mm110) REVERT: K 31 ASP cc_start: 0.7449 (p0) cc_final: 0.6932 (p0) REVERT: K 78 GLN cc_start: 0.5181 (mp10) cc_final: 0.4823 (pt0) REVERT: K 109 MET cc_start: 0.7422 (mmm) cc_final: 0.7175 (mmm) REVERT: K 110 ASP cc_start: 0.8182 (p0) cc_final: 0.7942 (p0) outliers start: 45 outliers final: 26 residues processed: 356 average time/residue: 0.1453 time to fit residues: 79.2516 Evaluate side-chains 335 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 304 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 324 ILE Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain L residue 21 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 40 optimal weight: 6.9990 chunk 161 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 143 optimal weight: 30.0000 chunk 152 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 224 optimal weight: 30.0000 chunk 6 optimal weight: 4.9990 chunk 198 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN D 79 GLN ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 ASN E 377 ASN E 469 HIS ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 353 HIS L 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.179471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.164739 restraints weight = 25846.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.163867 restraints weight = 44238.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.163258 restraints weight = 50649.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.162535 restraints weight = 43125.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.161756 restraints weight = 44735.760| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 20604 Z= 0.245 Angle : 0.767 11.312 27930 Z= 0.382 Chirality : 0.050 0.412 3048 Planarity : 0.005 0.057 3567 Dihedral : 10.602 67.386 3278 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.23 % Allowed : 14.06 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.16), residues: 2472 helix: 0.91 (0.21), residues: 591 sheet: -1.34 (0.22), residues: 546 loop : -1.77 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 19 TYR 0.022 0.002 TYR I 468 PHE 0.015 0.002 PHE I 415 TRP 0.031 0.002 TRP A 150 HIS 0.007 0.001 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00566 (20550) covalent geometry : angle 0.73417 (27795) SS BOND : bond 0.00769 ( 27) SS BOND : angle 2.17477 ( 54) hydrogen bonds : bond 0.05110 ( 774) hydrogen bonds : angle 5.54527 ( 2232) link_BETA1-4 : bond 0.01549 ( 12) link_BETA1-4 : angle 4.04934 ( 36) link_NAG-ASN : bond 0.00620 ( 15) link_NAG-ASN : angle 3.62842 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 329 time to evaluate : 0.554 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 24 ARG cc_start: 0.7577 (mmm-85) cc_final: 0.6895 (mtm180) REVERT: A 337 ILE cc_start: 0.9061 (mm) cc_final: 0.8684 (mm) REVERT: A 349 TYR cc_start: 0.9235 (OUTLIER) cc_final: 0.8420 (m-80) REVERT: A 411 MET cc_start: 0.9088 (tmm) cc_final: 0.8594 (tmm) REVERT: A 433 ARG cc_start: 0.7064 (OUTLIER) cc_final: 0.6209 (mtt-85) REVERT: A 476 MET cc_start: 0.7487 (mtp) cc_final: 0.7263 (mtp) REVERT: C 31 ASP cc_start: 0.7614 (p0) cc_final: 0.7407 (p0) REVERT: C 33 TYR cc_start: 0.8373 (m-80) cc_final: 0.8172 (m-80) REVERT: C 60 THR cc_start: 0.8649 (m) cc_final: 0.8248 (p) REVERT: C 78 GLN cc_start: 0.6173 (mp10) cc_final: 0.5699 (pt0) REVERT: E 115 LYS cc_start: 0.7393 (ttmt) cc_final: 0.7157 (ttpt) REVERT: E 337 ILE cc_start: 0.9222 (mm) cc_final: 0.8937 (mm) REVERT: E 411 MET cc_start: 0.8846 (tmm) cc_final: 0.8551 (tmm) REVERT: E 433 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6137 (tpt170) REVERT: E 466 GLU cc_start: 0.7815 (tt0) cc_final: 0.7593 (tt0) REVERT: E 468 TYR cc_start: 0.7966 (m-80) cc_final: 0.7538 (m-80) REVERT: G 12 VAL cc_start: 0.8305 (t) cc_final: 0.8043 (m) REVERT: G 31 ASP cc_start: 0.7791 (p0) cc_final: 0.7530 (p0) REVERT: G 75 ASP cc_start: 0.6139 (p0) cc_final: 0.5552 (p0) REVERT: G 109 MET cc_start: 0.7827 (mmm) cc_final: 0.7414 (mmm) REVERT: G 149 GLU cc_start: 0.2475 (mp0) cc_final: 0.2133 (mm-30) REVERT: I 115 LYS cc_start: 0.8319 (ttpp) cc_final: 0.8106 (ttpp) REVERT: I 324 ILE cc_start: 0.7528 (mt) cc_final: 0.7174 (pt) REVERT: I 429 MET cc_start: 0.7629 (mtt) cc_final: 0.7260 (mtt) REVERT: I 433 ARG cc_start: 0.6674 (OUTLIER) cc_final: 0.6439 (tpt170) REVERT: I 486 TYR cc_start: 0.8039 (t80) cc_final: 0.7782 (t80) REVERT: K 31 ASP cc_start: 0.7423 (p0) cc_final: 0.7121 (p0) REVERT: K 78 GLN cc_start: 0.5352 (mp10) cc_final: 0.5030 (pt0) REVERT: K 109 MET cc_start: 0.7855 (mmm) cc_final: 0.7455 (mmm) REVERT: L 74 LYS cc_start: 0.7161 (mtmm) cc_final: 0.6612 (mtmt) REVERT: L 91 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7750 (m-10) outliers start: 70 outliers final: 46 residues processed: 375 average time/residue: 0.1394 time to fit residues: 80.5886 Evaluate side-chains 342 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 291 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 278 LYS Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 278 LYS Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 393 VAL Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 96 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 91 optimal weight: 5.9990 chunk 175 optimal weight: 8.9990 chunk 213 optimal weight: 5.9990 chunk 7 optimal weight: 0.0060 chunk 31 optimal weight: 0.7980 chunk 154 optimal weight: 10.0000 chunk 160 optimal weight: 20.0000 chunk 169 optimal weight: 6.9990 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN E 469 HIS I 207 ASN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.188671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.174086 restraints weight = 25540.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.171646 restraints weight = 39714.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.170952 restraints weight = 51123.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.170089 restraints weight = 42210.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.169231 restraints weight = 45767.150| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 20604 Z= 0.154 Angle : 0.677 10.681 27930 Z= 0.335 Chirality : 0.046 0.400 3048 Planarity : 0.004 0.061 3567 Dihedral : 9.198 57.680 3274 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.86 % Allowed : 17.47 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.17), residues: 2472 helix: 1.14 (0.21), residues: 594 sheet: -1.32 (0.22), residues: 549 loop : -1.66 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 146 TYR 0.017 0.002 TYR H 145 PHE 0.012 0.002 PHE I 372 TRP 0.025 0.001 TRP A 150 HIS 0.004 0.001 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00347 (20550) covalent geometry : angle 0.64624 (27795) SS BOND : bond 0.00441 ( 27) SS BOND : angle 1.72860 ( 54) hydrogen bonds : bond 0.04490 ( 774) hydrogen bonds : angle 5.27810 ( 2232) link_BETA1-4 : bond 0.01377 ( 12) link_BETA1-4 : angle 3.66124 ( 36) link_NAG-ASN : bond 0.00623 ( 15) link_NAG-ASN : angle 3.48573 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 336 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7589 (mmm-85) cc_final: 0.6831 (mtm-85) REVERT: A 260 ARG cc_start: 0.7476 (tpp-160) cc_final: 0.6941 (tpp-160) REVERT: A 337 ILE cc_start: 0.9022 (mm) cc_final: 0.8635 (mm) REVERT: A 411 MET cc_start: 0.9136 (tmm) cc_final: 0.8386 (tmm) REVERT: A 433 ARG cc_start: 0.6929 (OUTLIER) cc_final: 0.6064 (mtt-85) REVERT: C 31 ASP cc_start: 0.7523 (p0) cc_final: 0.7148 (p0) REVERT: C 34 MET cc_start: 0.7774 (tpp) cc_final: 0.7085 (tpp) REVERT: C 60 THR cc_start: 0.8496 (m) cc_final: 0.8260 (p) REVERT: C 144 LEU cc_start: 0.5570 (mp) cc_final: 0.5246 (tt) REVERT: D 74 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.7215 (mmtt) REVERT: E 115 LYS cc_start: 0.7348 (ttmt) cc_final: 0.6908 (ttmt) REVERT: E 324 ILE cc_start: 0.6817 (mt) cc_final: 0.6592 (pt) REVERT: E 337 ILE cc_start: 0.9138 (mm) cc_final: 0.8901 (mm) REVERT: E 411 MET cc_start: 0.8709 (tmm) cc_final: 0.8494 (tmm) REVERT: E 433 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.6064 (tpt170) REVERT: E 466 GLU cc_start: 0.7749 (tt0) cc_final: 0.7479 (tt0) REVERT: E 468 TYR cc_start: 0.7843 (m-80) cc_final: 0.7420 (m-80) REVERT: G 12 VAL cc_start: 0.8239 (t) cc_final: 0.8002 (m) REVERT: G 109 MET cc_start: 0.7786 (mmm) cc_final: 0.7530 (mmm) REVERT: G 149 GLU cc_start: 0.2593 (mp0) cc_final: 0.1734 (mm-30) REVERT: I 324 ILE cc_start: 0.7578 (mt) cc_final: 0.7252 (pt) REVERT: I 337 ILE cc_start: 0.9047 (mm) cc_final: 0.8799 (mm) REVERT: I 355 ASN cc_start: 0.8562 (t0) cc_final: 0.8258 (t0) REVERT: I 429 MET cc_start: 0.7484 (mtt) cc_final: 0.7119 (mtt) REVERT: I 486 TYR cc_start: 0.8147 (t80) cc_final: 0.7886 (t80) REVERT: K 31 ASP cc_start: 0.7417 (p0) cc_final: 0.6959 (p0) REVERT: K 109 MET cc_start: 0.7806 (mmm) cc_final: 0.7565 (mmm) REVERT: L 74 LYS cc_start: 0.7292 (mtmm) cc_final: 0.6627 (mtmt) outliers start: 62 outliers final: 44 residues processed: 374 average time/residue: 0.1429 time to fit residues: 82.5342 Evaluate side-chains 341 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 294 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 278 LYS Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 278 LYS Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 308 LYS Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 139 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 168 optimal weight: 0.9980 chunk 149 optimal weight: 9.9990 chunk 201 optimal weight: 4.9990 chunk 146 optimal weight: 30.0000 chunk 76 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN E 408 ASN ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 207 ASN L 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.185344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.178081 restraints weight = 25381.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.162051 restraints weight = 45997.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.158618 restraints weight = 68826.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.158250 restraints weight = 53691.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.158269 restraints weight = 44005.549| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 20604 Z= 0.252 Angle : 0.755 11.382 27930 Z= 0.374 Chirality : 0.048 0.418 3048 Planarity : 0.005 0.060 3567 Dihedral : 8.644 57.096 3269 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 3.92 % Allowed : 18.53 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.16), residues: 2472 helix: 0.93 (0.21), residues: 594 sheet: -1.39 (0.22), residues: 552 loop : -1.72 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 433 TYR 0.032 0.002 TYR C 82 PHE 0.017 0.002 PHE K 50 TRP 0.035 0.002 TRP A 150 HIS 0.005 0.001 HIS E 353 Details of bonding type rmsd covalent geometry : bond 0.00590 (20550) covalent geometry : angle 0.72269 (27795) SS BOND : bond 0.00650 ( 27) SS BOND : angle 2.09950 ( 54) hydrogen bonds : bond 0.04851 ( 774) hydrogen bonds : angle 5.38539 ( 2232) link_BETA1-4 : bond 0.01682 ( 12) link_BETA1-4 : angle 3.87236 ( 36) link_NAG-ASN : bond 0.00573 ( 15) link_NAG-ASN : angle 3.78995 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 311 time to evaluate : 0.532 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 24 ARG cc_start: 0.7541 (mmm-85) cc_final: 0.6807 (mtm180) REVERT: A 337 ILE cc_start: 0.9048 (mm) cc_final: 0.8644 (mm) REVERT: A 349 TYR cc_start: 0.9288 (OUTLIER) cc_final: 0.8482 (m-80) REVERT: A 411 MET cc_start: 0.8985 (tmm) cc_final: 0.8189 (tmm) REVERT: A 433 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6170 (mmt180) REVERT: C 31 ASP cc_start: 0.7724 (p0) cc_final: 0.7447 (p0) REVERT: C 34 MET cc_start: 0.8034 (tpp) cc_final: 0.7832 (tpp) REVERT: C 60 THR cc_start: 0.8762 (m) cc_final: 0.8425 (p) REVERT: D 69 THR cc_start: 0.6920 (p) cc_final: 0.6550 (p) REVERT: E 63 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8708 (mm) REVERT: E 115 LYS cc_start: 0.7377 (ttmt) cc_final: 0.6905 (ttmt) REVERT: E 337 ILE cc_start: 0.9137 (mm) cc_final: 0.8873 (mm) REVERT: E 349 TYR cc_start: 0.9110 (OUTLIER) cc_final: 0.8247 (m-80) REVERT: E 425 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8918 (tp) REVERT: E 433 ARG cc_start: 0.7276 (tpp80) cc_final: 0.6678 (tpt-90) REVERT: E 468 TYR cc_start: 0.7995 (m-80) cc_final: 0.7451 (m-80) REVERT: G 12 VAL cc_start: 0.8296 (t) cc_final: 0.8018 (m) REVERT: G 84 GLN cc_start: 0.7620 (mm110) cc_final: 0.7411 (mm110) REVERT: G 109 MET cc_start: 0.7931 (mmm) cc_final: 0.7594 (mmm) REVERT: G 149 GLU cc_start: 0.2387 (mp0) cc_final: 0.1597 (mm-30) REVERT: I 43 LEU cc_start: 0.7373 (mm) cc_final: 0.6848 (mt) REVERT: I 324 ILE cc_start: 0.7602 (mt) cc_final: 0.7250 (pt) REVERT: I 337 ILE cc_start: 0.9101 (mm) cc_final: 0.8855 (mm) REVERT: I 355 ASN cc_start: 0.8659 (t0) cc_final: 0.8423 (t0) REVERT: I 429 MET cc_start: 0.7665 (mtt) cc_final: 0.7391 (mtt) REVERT: I 486 TYR cc_start: 0.8221 (t80) cc_final: 0.7923 (t80) REVERT: K 31 ASP cc_start: 0.7461 (p0) cc_final: 0.6928 (p0) REVERT: K 109 MET cc_start: 0.7968 (mmm) cc_final: 0.7516 (mmm) REVERT: K 147 MET cc_start: 0.4009 (ptt) cc_final: 0.3442 (ptt) REVERT: L 74 LYS cc_start: 0.7183 (mtmm) cc_final: 0.6514 (mtmt) REVERT: L 91 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.8079 (m-10) REVERT: L 134 MET cc_start: 0.2995 (mtp) cc_final: 0.2268 (mtp) outliers start: 85 outliers final: 61 residues processed: 368 average time/residue: 0.1365 time to fit residues: 78.7963 Evaluate side-chains 356 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 289 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 278 LYS Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 349 TYR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 425 LEU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 278 LYS Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 308 LYS Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain I residue 393 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 145 optimal weight: 30.0000 chunk 57 optimal weight: 20.0000 chunk 136 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 13 optimal weight: 0.0980 chunk 191 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 179 optimal weight: 5.9990 chunk 211 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 HIS ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.189845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.182482 restraints weight = 25234.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.168542 restraints weight = 43900.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.164867 restraints weight = 67867.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.163992 restraints weight = 66656.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.163957 restraints weight = 52043.052| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20604 Z= 0.138 Angle : 0.662 10.680 27930 Z= 0.327 Chirality : 0.046 0.399 3048 Planarity : 0.004 0.061 3567 Dihedral : 7.777 59.701 3260 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.90 % Allowed : 20.52 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.17), residues: 2472 helix: 1.14 (0.21), residues: 600 sheet: -1.31 (0.22), residues: 549 loop : -1.59 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 126 TYR 0.027 0.002 TYR C 82 PHE 0.012 0.001 PHE A 372 TRP 0.024 0.001 TRP A 150 HIS 0.007 0.001 HIS E 469 Details of bonding type rmsd covalent geometry : bond 0.00309 (20550) covalent geometry : angle 0.63087 (27795) SS BOND : bond 0.00389 ( 27) SS BOND : angle 1.78417 ( 54) hydrogen bonds : bond 0.04335 ( 774) hydrogen bonds : angle 5.18619 ( 2232) link_BETA1-4 : bond 0.01467 ( 12) link_BETA1-4 : angle 3.60185 ( 36) link_NAG-ASN : bond 0.00616 ( 15) link_NAG-ASN : angle 3.50570 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 311 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7549 (mmm-85) cc_final: 0.6769 (mtm-85) REVERT: A 114 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6996 (mt-10) REVERT: A 337 ILE cc_start: 0.9012 (mm) cc_final: 0.8638 (mm) REVERT: A 349 TYR cc_start: 0.9272 (OUTLIER) cc_final: 0.8411 (m-80) REVERT: A 411 MET cc_start: 0.9102 (tmm) cc_final: 0.8404 (tmm) REVERT: A 429 MET cc_start: 0.6796 (mtp) cc_final: 0.6089 (mtt) REVERT: A 433 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.6254 (mmt90) REVERT: C 31 ASP cc_start: 0.7582 (p0) cc_final: 0.7260 (p0) REVERT: C 34 MET cc_start: 0.8038 (tpp) cc_final: 0.7689 (tpp) REVERT: C 60 THR cc_start: 0.8553 (m) cc_final: 0.8250 (p) REVERT: C 109 MET cc_start: 0.7627 (mmm) cc_final: 0.7387 (mmm) REVERT: C 110 ASP cc_start: 0.8476 (p0) cc_final: 0.8021 (p0) REVERT: D 69 THR cc_start: 0.6776 (p) cc_final: 0.6468 (p) REVERT: E 213 GLU cc_start: 0.7640 (pm20) cc_final: 0.6760 (pm20) REVERT: E 349 TYR cc_start: 0.9079 (OUTLIER) cc_final: 0.8440 (m-80) REVERT: E 366 GLU cc_start: 0.6785 (tt0) cc_final: 0.6380 (tt0) REVERT: E 429 MET cc_start: 0.7473 (mtp) cc_final: 0.7175 (mtt) REVERT: E 433 ARG cc_start: 0.7182 (tpp80) cc_final: 0.6525 (tpt-90) REVERT: E 468 TYR cc_start: 0.7854 (m-80) cc_final: 0.7349 (m-80) REVERT: G 12 VAL cc_start: 0.8035 (t) cc_final: 0.7705 (m) REVERT: G 109 MET cc_start: 0.7952 (mmm) cc_final: 0.7581 (mmm) REVERT: G 149 GLU cc_start: 0.2936 (mp0) cc_final: 0.2084 (mm-30) REVERT: I 43 LEU cc_start: 0.7189 (mm) cc_final: 0.6628 (mt) REVERT: I 324 ILE cc_start: 0.7623 (mt) cc_final: 0.7250 (pt) REVERT: I 337 ILE cc_start: 0.9075 (mm) cc_final: 0.8768 (mm) REVERT: I 355 ASN cc_start: 0.8584 (t0) cc_final: 0.8262 (t0) REVERT: I 429 MET cc_start: 0.7554 (mtt) cc_final: 0.7323 (mtt) REVERT: K 109 MET cc_start: 0.7861 (mmm) cc_final: 0.7570 (mmm) REVERT: K 144 LEU cc_start: 0.5632 (mp) cc_final: 0.5290 (tt) REVERT: L 74 LYS cc_start: 0.6906 (mtmm) cc_final: 0.6207 (mtmt) REVERT: L 134 MET cc_start: 0.2975 (mtp) cc_final: 0.2393 (mtp) outliers start: 63 outliers final: 46 residues processed: 352 average time/residue: 0.1350 time to fit residues: 74.3351 Evaluate side-chains 341 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 291 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 278 LYS Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 349 TYR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 66 ASN Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 308 LYS Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 27 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 239 optimal weight: 20.0000 chunk 182 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 134 optimal weight: 0.0670 chunk 128 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.178207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.168253 restraints weight = 26073.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.167318 restraints weight = 46139.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.166594 restraints weight = 51345.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.165856 restraints weight = 50779.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.165331 restraints weight = 49092.005| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20604 Z= 0.228 Angle : 0.718 11.146 27930 Z= 0.356 Chirality : 0.047 0.413 3048 Planarity : 0.005 0.062 3567 Dihedral : 7.715 48.605 3260 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.50 % Allowed : 21.21 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.17), residues: 2472 helix: 1.01 (0.21), residues: 600 sheet: -1.34 (0.22), residues: 552 loop : -1.65 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 126 TYR 0.022 0.002 TYR G 107 PHE 0.016 0.002 PHE I 372 TRP 0.033 0.002 TRP A 150 HIS 0.017 0.002 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00530 (20550) covalent geometry : angle 0.68735 (27795) SS BOND : bond 0.00705 ( 27) SS BOND : angle 1.69361 ( 54) hydrogen bonds : bond 0.04626 ( 774) hydrogen bonds : angle 5.23857 ( 2232) link_BETA1-4 : bond 0.01576 ( 12) link_BETA1-4 : angle 3.79183 ( 36) link_NAG-ASN : bond 0.00542 ( 15) link_NAG-ASN : angle 3.67121 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 294 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7560 (mmm-85) cc_final: 0.6805 (mtm-85) REVERT: A 302 GLU cc_start: 0.6352 (tp30) cc_final: 0.6071 (tp30) REVERT: A 337 ILE cc_start: 0.9049 (mm) cc_final: 0.8642 (mm) REVERT: A 349 TYR cc_start: 0.9238 (OUTLIER) cc_final: 0.8368 (m-80) REVERT: A 411 MET cc_start: 0.8939 (tmm) cc_final: 0.8263 (tmm) REVERT: A 433 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6174 (mmt180) REVERT: C 31 ASP cc_start: 0.7681 (p0) cc_final: 0.7426 (p0) REVERT: C 34 MET cc_start: 0.8052 (tpp) cc_final: 0.7688 (tpp) REVERT: C 60 THR cc_start: 0.8730 (m) cc_final: 0.8331 (p) REVERT: C 109 MET cc_start: 0.7795 (mmm) cc_final: 0.7514 (mmm) REVERT: D 69 THR cc_start: 0.6551 (p) cc_final: 0.6208 (p) REVERT: E 247 ASN cc_start: 0.8605 (m110) cc_final: 0.8096 (m-40) REVERT: E 349 TYR cc_start: 0.9130 (OUTLIER) cc_final: 0.8366 (m-80) REVERT: E 425 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8877 (tp) REVERT: E 468 TYR cc_start: 0.7958 (m-80) cc_final: 0.7454 (m-80) REVERT: G 31 ASP cc_start: 0.7540 (p0) cc_final: 0.7304 (p0) REVERT: G 109 MET cc_start: 0.8009 (mmm) cc_final: 0.7604 (mmm) REVERT: G 149 GLU cc_start: 0.2417 (mp0) cc_final: 0.1655 (mm-30) REVERT: H 70 GLN cc_start: 0.7746 (tp-100) cc_final: 0.7464 (tp40) REVERT: I 43 LEU cc_start: 0.7391 (mm) cc_final: 0.6993 (mt) REVERT: I 324 ILE cc_start: 0.7451 (mt) cc_final: 0.7202 (pt) REVERT: I 337 ILE cc_start: 0.9118 (mm) cc_final: 0.8869 (mm) REVERT: I 355 ASN cc_start: 0.8646 (t0) cc_final: 0.8326 (t0) REVERT: I 429 MET cc_start: 0.7809 (mtt) cc_final: 0.7582 (mtt) REVERT: I 486 TYR cc_start: 0.8285 (t80) cc_final: 0.7774 (t80) REVERT: K 109 MET cc_start: 0.7901 (mmm) cc_final: 0.7649 (mmm) REVERT: L 74 LYS cc_start: 0.6542 (mtmm) cc_final: 0.5764 (mtmt) REVERT: L 134 MET cc_start: 0.3529 (mtp) cc_final: 0.3086 (mtp) outliers start: 76 outliers final: 61 residues processed: 346 average time/residue: 0.1269 time to fit residues: 69.8517 Evaluate side-chains 353 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 288 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 278 LYS Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 349 TYR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 425 LEU Chi-restraints excluded: chain E residue 475 CYS Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 66 ASN Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 278 LYS Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 308 LYS Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain I residue 393 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 233 optimal weight: 7.9990 chunk 39 optimal weight: 0.0270 chunk 96 optimal weight: 0.9980 chunk 153 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 198 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 overall best weight: 2.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.185068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.177994 restraints weight = 25619.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.176947 restraints weight = 46527.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.175741 restraints weight = 58969.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.174933 restraints weight = 52570.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.174092 restraints weight = 55175.982| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20604 Z= 0.164 Angle : 0.673 10.766 27930 Z= 0.333 Chirality : 0.046 0.404 3048 Planarity : 0.005 0.063 3567 Dihedral : 7.182 44.619 3260 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.32 % Allowed : 21.25 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.17), residues: 2472 helix: 1.12 (0.21), residues: 600 sheet: -1.26 (0.22), residues: 549 loop : -1.60 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 19 TYR 0.022 0.002 TYR C 82 PHE 0.013 0.002 PHE A 372 TRP 0.028 0.001 TRP A 150 HIS 0.003 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00376 (20550) covalent geometry : angle 0.64303 (27795) SS BOND : bond 0.00543 ( 27) SS BOND : angle 1.41299 ( 54) hydrogen bonds : bond 0.04343 ( 774) hydrogen bonds : angle 5.13832 ( 2232) link_BETA1-4 : bond 0.01480 ( 12) link_BETA1-4 : angle 3.66566 ( 36) link_NAG-ASN : bond 0.00583 ( 15) link_NAG-ASN : angle 3.53477 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 304 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7539 (mmm-85) cc_final: 0.6777 (mtm-85) REVERT: A 63 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8112 (mm) REVERT: A 302 GLU cc_start: 0.6314 (tp30) cc_final: 0.5822 (tp30) REVERT: A 337 ILE cc_start: 0.9033 (mm) cc_final: 0.8625 (mm) REVERT: A 349 TYR cc_start: 0.9247 (OUTLIER) cc_final: 0.8431 (m-80) REVERT: A 366 GLU cc_start: 0.6831 (tt0) cc_final: 0.6440 (tt0) REVERT: A 411 MET cc_start: 0.9111 (tmm) cc_final: 0.8518 (tmm) REVERT: A 433 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.6067 (mmt180) REVERT: C 31 ASP cc_start: 0.7812 (p0) cc_final: 0.7574 (p0) REVERT: C 34 MET cc_start: 0.8004 (tpp) cc_final: 0.7594 (tpp) REVERT: C 60 THR cc_start: 0.8615 (m) cc_final: 0.8248 (p) REVERT: D 69 THR cc_start: 0.6446 (p) cc_final: 0.6133 (p) REVERT: E 162 LYS cc_start: 0.6911 (tppp) cc_final: 0.6570 (tptp) REVERT: E 247 ASN cc_start: 0.8684 (m110) cc_final: 0.8376 (m-40) REVERT: E 265 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8505 (mt) REVERT: E 349 TYR cc_start: 0.9025 (OUTLIER) cc_final: 0.8103 (m-80) REVERT: E 366 GLU cc_start: 0.6777 (tt0) cc_final: 0.6520 (tt0) REVERT: E 433 ARG cc_start: 0.6193 (mmm160) cc_final: 0.5989 (mmm-85) REVERT: E 468 TYR cc_start: 0.7853 (m-80) cc_final: 0.7396 (m-80) REVERT: G 109 MET cc_start: 0.7989 (mmm) cc_final: 0.7566 (mmm) REVERT: G 149 GLU cc_start: 0.2859 (mp0) cc_final: 0.1831 (mm-30) REVERT: I 43 LEU cc_start: 0.7335 (mm) cc_final: 0.6796 (mt) REVERT: I 324 ILE cc_start: 0.7357 (mt) cc_final: 0.7144 (pt) REVERT: I 337 ILE cc_start: 0.9096 (mm) cc_final: 0.8856 (mm) REVERT: I 355 ASN cc_start: 0.8611 (t0) cc_final: 0.8284 (t0) REVERT: I 429 MET cc_start: 0.7623 (mtt) cc_final: 0.7342 (mtt) REVERT: L 74 LYS cc_start: 0.6520 (mtmm) cc_final: 0.5747 (mtmt) REVERT: L 91 PHE cc_start: 0.8410 (m-80) cc_final: 0.8171 (m-10) outliers start: 72 outliers final: 53 residues processed: 353 average time/residue: 0.1364 time to fit residues: 75.8936 Evaluate side-chains 350 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 292 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 278 LYS Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 349 TYR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 387 ASN Chi-restraints excluded: chain E residue 475 CYS Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 66 ASN Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 308 LYS Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain I residue 393 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 118 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 2 optimal weight: 7.9990 chunk 209 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 236 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 HIS ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN H 79 GLN I 207 ASN L 53 ASN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.180686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.171773 restraints weight = 25729.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.169536 restraints weight = 47205.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.168187 restraints weight = 64077.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.154389 restraints weight = 59252.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.151050 restraints weight = 51755.913| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 20604 Z= 0.261 Angle : 0.753 11.444 27930 Z= 0.376 Chirality : 0.048 0.422 3048 Planarity : 0.005 0.062 3567 Dihedral : 7.382 45.036 3260 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 3.64 % Allowed : 21.07 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.16), residues: 2472 helix: 0.90 (0.21), residues: 600 sheet: -1.35 (0.22), residues: 552 loop : -1.76 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 19 TYR 0.024 0.002 TYR G 107 PHE 0.019 0.002 PHE H 62 TRP 0.045 0.002 TRP A 150 HIS 0.005 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00608 (20550) covalent geometry : angle 0.72132 (27795) SS BOND : bond 0.00722 ( 27) SS BOND : angle 1.82933 ( 54) hydrogen bonds : bond 0.04776 ( 774) hydrogen bonds : angle 5.28738 ( 2232) link_BETA1-4 : bond 0.01635 ( 12) link_BETA1-4 : angle 3.88851 ( 36) link_NAG-ASN : bond 0.00535 ( 15) link_NAG-ASN : angle 3.76010 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 299 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7492 (mmm-85) cc_final: 0.6740 (mtm-85) REVERT: A 63 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8379 (mm) REVERT: A 302 GLU cc_start: 0.6598 (tp30) cc_final: 0.6108 (tp30) REVERT: A 337 ILE cc_start: 0.9056 (mm) cc_final: 0.8670 (mm) REVERT: A 349 TYR cc_start: 0.9283 (OUTLIER) cc_final: 0.8482 (m-80) REVERT: A 366 GLU cc_start: 0.7058 (tt0) cc_final: 0.6754 (tt0) REVERT: A 411 MET cc_start: 0.8916 (tmm) cc_final: 0.8192 (tmm) REVERT: A 433 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6710 (mpt180) REVERT: C 31 ASP cc_start: 0.7946 (p0) cc_final: 0.7667 (p0) REVERT: C 34 MET cc_start: 0.8204 (tpp) cc_final: 0.7542 (tpp) REVERT: C 60 THR cc_start: 0.8793 (m) cc_final: 0.8380 (p) REVERT: D 69 THR cc_start: 0.7082 (p) cc_final: 0.6763 (p) REVERT: E 56 ASP cc_start: 0.5672 (t0) cc_final: 0.5364 (t0) REVERT: E 162 LYS cc_start: 0.7072 (tppp) cc_final: 0.6618 (tptp) REVERT: E 247 ASN cc_start: 0.8754 (m110) cc_final: 0.8349 (m-40) REVERT: E 265 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8806 (mt) REVERT: E 355 ASN cc_start: 0.8670 (t0) cc_final: 0.8428 (t0) REVERT: E 366 GLU cc_start: 0.6928 (tt0) cc_final: 0.6705 (tt0) REVERT: E 425 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8802 (tp) REVERT: E 468 TYR cc_start: 0.8182 (m-80) cc_final: 0.7393 (m-80) REVERT: G 109 MET cc_start: 0.8198 (mmm) cc_final: 0.7775 (mmm) REVERT: G 149 GLU cc_start: 0.3129 (mp0) cc_final: 0.2144 (mm-30) REVERT: H 79 GLN cc_start: 0.4517 (OUTLIER) cc_final: 0.4306 (tm-30) REVERT: I 43 LEU cc_start: 0.7257 (mm) cc_final: 0.6940 (mt) REVERT: I 52 LEU cc_start: 0.8851 (tt) cc_final: 0.8365 (tp) REVERT: I 53 GLU cc_start: 0.7290 (tp30) cc_final: 0.6942 (tp30) REVERT: I 337 ILE cc_start: 0.9169 (mm) cc_final: 0.8940 (mm) REVERT: I 355 ASN cc_start: 0.8687 (t0) cc_final: 0.8368 (t0) REVERT: I 429 MET cc_start: 0.7662 (mtt) cc_final: 0.7341 (mtt) REVERT: I 486 TYR cc_start: 0.8377 (t80) cc_final: 0.7866 (t80) REVERT: K 110 ASP cc_start: 0.8259 (p0) cc_final: 0.7811 (p0) REVERT: K 144 LEU cc_start: 0.4602 (tt) cc_final: 0.4342 (mt) REVERT: L 74 LYS cc_start: 0.7030 (mtmm) cc_final: 0.6190 (mtmt) outliers start: 79 outliers final: 63 residues processed: 356 average time/residue: 0.1361 time to fit residues: 75.6718 Evaluate side-chains 361 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 292 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 278 LYS Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 349 TYR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 387 ASN Chi-restraints excluded: chain E residue 425 LEU Chi-restraints excluded: chain E residue 475 CYS Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 66 ASN Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 308 LYS Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain I residue 393 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 32 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 237 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 53 optimal weight: 0.0370 chunk 232 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 214 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 ASN ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 ASN H 79 GLN K 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.177433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.163808 restraints weight = 25475.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.161809 restraints weight = 47232.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.160843 restraints weight = 60579.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.159937 restraints weight = 49715.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.159575 restraints weight = 54631.099| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 20604 Z= 0.129 Angle : 0.662 10.391 27930 Z= 0.330 Chirality : 0.045 0.395 3048 Planarity : 0.005 0.063 3567 Dihedral : 6.641 48.843 3260 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.26 % Allowed : 22.41 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.17), residues: 2472 helix: 1.28 (0.21), residues: 600 sheet: -1.28 (0.22), residues: 549 loop : -1.56 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 19 TYR 0.029 0.002 TYR C 82 PHE 0.012 0.001 PHE I 372 TRP 0.031 0.001 TRP I 78 HIS 0.004 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00287 (20550) covalent geometry : angle 0.63379 (27795) SS BOND : bond 0.00425 ( 27) SS BOND : angle 1.14731 ( 54) hydrogen bonds : bond 0.04141 ( 774) hydrogen bonds : angle 5.05908 ( 2232) link_BETA1-4 : bond 0.01433 ( 12) link_BETA1-4 : angle 3.59090 ( 36) link_NAG-ASN : bond 0.00641 ( 15) link_NAG-ASN : angle 3.40470 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 316 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7446 (mmm-85) cc_final: 0.6708 (mtm-85) REVERT: A 63 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8107 (mm) REVERT: A 83 GLU cc_start: 0.7507 (tt0) cc_final: 0.7198 (tt0) REVERT: A 302 GLU cc_start: 0.6351 (tp30) cc_final: 0.5823 (tp30) REVERT: A 337 ILE cc_start: 0.9022 (mm) cc_final: 0.8625 (mm) REVERT: A 349 TYR cc_start: 0.9178 (OUTLIER) cc_final: 0.8398 (m-80) REVERT: A 366 GLU cc_start: 0.6759 (tt0) cc_final: 0.6287 (tt0) REVERT: A 411 MET cc_start: 0.9095 (tmm) cc_final: 0.8516 (tmm) REVERT: A 429 MET cc_start: 0.6913 (mtp) cc_final: 0.6109 (mtt) REVERT: A 433 ARG cc_start: 0.6960 (OUTLIER) cc_final: 0.5912 (mmt180) REVERT: A 476 MET cc_start: 0.8302 (ttm) cc_final: 0.7849 (tpp) REVERT: C 34 MET cc_start: 0.7945 (tpp) cc_final: 0.7687 (tpp) REVERT: C 60 THR cc_start: 0.8461 (m) cc_final: 0.8100 (p) REVERT: C 74 ARG cc_start: 0.7329 (ptp-170) cc_final: 0.6703 (ptm160) REVERT: D 69 THR cc_start: 0.6475 (p) cc_final: 0.6156 (p) REVERT: D 134 MET cc_start: 0.3421 (mtp) cc_final: 0.2802 (mtm) REVERT: E 73 LEU cc_start: 0.5611 (mm) cc_final: 0.5056 (mt) REVERT: E 162 LYS cc_start: 0.6904 (tppp) cc_final: 0.6467 (tptp) REVERT: E 247 ASN cc_start: 0.8626 (m110) cc_final: 0.8422 (m-40) REVERT: E 355 ASN cc_start: 0.8510 (t0) cc_final: 0.8231 (t0) REVERT: E 366 GLU cc_start: 0.6681 (tt0) cc_final: 0.6400 (tt0) REVERT: G 109 MET cc_start: 0.7902 (mmm) cc_final: 0.7491 (mmm) REVERT: G 149 GLU cc_start: 0.2901 (mp0) cc_final: 0.1857 (mm-30) REVERT: I 43 LEU cc_start: 0.7107 (mm) cc_final: 0.6615 (mt) REVERT: I 52 LEU cc_start: 0.8702 (tt) cc_final: 0.8301 (tp) REVERT: I 191 LEU cc_start: 0.7930 (mt) cc_final: 0.7690 (mt) REVERT: I 313 VAL cc_start: 0.9193 (t) cc_final: 0.8973 (m) REVERT: I 337 ILE cc_start: 0.9100 (mm) cc_final: 0.8885 (mm) REVERT: I 355 ASN cc_start: 0.8469 (t0) cc_final: 0.8201 (t0) REVERT: I 429 MET cc_start: 0.7549 (mtt) cc_final: 0.7310 (mtt) REVERT: L 12 SER cc_start: 0.6932 (t) cc_final: 0.6530 (t) REVERT: L 74 LYS cc_start: 0.6577 (mtmm) cc_final: 0.5841 (mtmt) REVERT: L 78 LEU cc_start: 0.5617 (OUTLIER) cc_final: 0.5410 (tt) outliers start: 49 outliers final: 38 residues processed: 347 average time/residue: 0.1397 time to fit residues: 75.4259 Evaluate side-chains 337 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 295 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 278 LYS Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 387 ASN Chi-restraints excluded: chain E residue 475 CYS Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 66 ASN Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 308 LYS Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain I residue 393 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 78 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 240 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 204 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 212 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 0.0050 chunk 118 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.177130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.163452 restraints weight = 25472.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.161234 restraints weight = 48308.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.160023 restraints weight = 59300.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.158734 restraints weight = 54550.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.158063 restraints weight = 57080.631| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20604 Z= 0.135 Angle : 0.657 10.937 27930 Z= 0.325 Chirality : 0.045 0.388 3048 Planarity : 0.005 0.061 3567 Dihedral : 6.226 50.471 3260 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.94 % Allowed : 22.41 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.17), residues: 2472 helix: 1.36 (0.21), residues: 600 sheet: -1.14 (0.23), residues: 537 loop : -1.54 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 74 TYR 0.030 0.002 TYR C 82 PHE 0.015 0.001 PHE H 91 TRP 0.027 0.001 TRP I 78 HIS 0.005 0.001 HIS E 469 Details of bonding type rmsd covalent geometry : bond 0.00304 (20550) covalent geometry : angle 0.62773 (27795) SS BOND : bond 0.00436 ( 27) SS BOND : angle 1.36220 ( 54) hydrogen bonds : bond 0.04089 ( 774) hydrogen bonds : angle 4.99639 ( 2232) link_BETA1-4 : bond 0.01542 ( 12) link_BETA1-4 : angle 3.71139 ( 36) link_NAG-ASN : bond 0.00619 ( 15) link_NAG-ASN : angle 3.30591 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2885.31 seconds wall clock time: 51 minutes 0.73 seconds (3060.73 seconds total)