Starting phenix.real_space_refine on Sat Jul 4 09:30:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dkj_30707/07_2026/7dkj_30707.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dkj_30707/07_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_30707/07_2026/7dkj_30707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dkj_30707/07_2026/7dkj_30707.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dkj_30707/07_2026/7dkj_30707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dkj_30707/07_2026/7dkj_30707.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7dkj_30707/07_2026/7dkj_30707.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dkj_30707/07_2026/7dkj_30707.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 chiralities: 3 Time building chain proxies: 4.80, per 1000 atoms: 0.24 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: 1.93 Conformation dependent library (CDL) restraints added in 959.2 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: 0.58 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: 3.85 Time building geometry restraints manager: 2.55 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 - 17.86: 10686 17.86 - 35.71: 1087 35.71 - 53.57: 232 53.57 - 71.42: 75 71.42 - 89.28: 46 Dihedral angle restraints: 12126 sinusoidal: 4974 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 12123 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: 0.06 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: 0.340 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: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.900 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 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 : 16.083 89.281 7485 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/Z covalent geometry : bond 0.00745 / 0.33 (20550) covalent geometry : angle 0.87271 / 0.46 (27795) SS BOND : bond 0.04307 / 3.72 ( 27) SS BOND : angle 1.99002 / 1.62 ( 54) hydrogen bonds : bond 0.16516 / 11.12 ( 774) hydrogen bonds : angle 8.30846 / 5.79 ( 2232) link_BETA1-4 : bond 0.01318 / 0.75 ( 12) link_BETA1-4 : angle 3.17871 / 2.37 ( 36) link_NAG-ASN : bond 0.00350 / 0.22 ( 15) link_NAG-ASN : angle 3.90330 / 2.75 ( 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 : 0.736 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: 0.1527 time to fit residues: 104.4937 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 : 0.733 ------------------------------------------------------------------------------- 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... ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 353 HIS 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 K 157 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.190848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.183556 restraints weight = 25421.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.182687 restraints weight = 46851.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.164594 restraints weight = 51619.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.163587 restraints weight = 58031.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.163340 restraints weight = 44572.202| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20604 Z= 0.170 Angle : 0.726 10.927 27930 Z= 0.373 Chirality : 0.048 0.404 3048 Planarity : 0.005 0.055 3567 Dihedral : 6.445 59.896 2749 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % 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: -1.54 (0.16), residues: 2472 helix: 0.71 (0.22), residues: 591 sheet: -1.24 (0.22), residues: 534 loop : -1.76 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 260 TYR 0.021 0.002 TYR K 62 PHE 0.012 0.002 PHE I 372 TRP 0.023 0.002 TRP E 150 HIS 0.012 0.002 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (20550) covalent geometry : angle 0.70219 / 0.37 (27795) SS BOND : bond 0.00491 / 0.35 ( 27) SS BOND : angle 1.96306 / 1.33 ( 54) hydrogen bonds : bond 0.05105 / 3.57 ( 774) hydrogen bonds : angle 5.75613 / 3.98 ( 2232) link_BETA1-4 : bond 0.01360 / 0.77 ( 12) link_BETA1-4 : angle 2.85202 / 2.10 ( 36) link_NAG-ASN : bond 0.00610 / 0.37 ( 15) link_NAG-ASN : angle 3.36892 / 2.41 ( 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 379 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 334 time to evaluate : 0.755 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: 0.8023 (mm) cc_final: 0.7724 (tp) REVERT: A 36 GLU cc_start: 0.7126 (tp30) cc_final: 0.6868 (tp30) REVERT: A 56 ASP cc_start: 0.4698 (t0) cc_final: 0.4463 (t0) REVERT: A 337 ILE cc_start: 0.8969 (mm) cc_final: 0.8585 (mm) REVERT: A 411 MET cc_start: 0.8958 (tmm) cc_final: 0.8445 (tmm) REVERT: A 412 GLU cc_start: 0.7191 (tt0) cc_final: 0.6529 (mt-10) REVERT: A 433 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6090 (mtt-85) REVERT: C 60 THR cc_start: 0.8294 (m) cc_final: 0.7738 (p) REVERT: C 78 GLN cc_start: 0.6378 (mp10) cc_final: 0.5660 (pt0) REVERT: C 109 MET cc_start: 0.8133 (mmm) cc_final: 0.7893 (mmm) REVERT: C 144 LEU cc_start: 0.4683 (tt) cc_final: 0.4425 (mp) REVERT: E 115 LYS cc_start: 0.7379 (ttmt) cc_final: 0.6825 (ttmt) REVERT: E 191 LEU cc_start: 0.7886 (mt) cc_final: 0.7219 (mt) REVERT: E 271 THR cc_start: 0.8428 (t) cc_final: 0.8073 (m) REVERT: E 308 LYS cc_start: 0.8448 (mtpp) cc_final: 0.8095 (mttm) REVERT: E 324 ILE cc_start: 0.6487 (OUTLIER) cc_final: 0.6238 (pt) REVERT: E 337 ILE cc_start: 0.9064 (mm) cc_final: 0.8730 (mm) REVERT: E 341 TRP cc_start: 0.8635 (m-10) cc_final: 0.7386 (m-10) REVERT: E 411 MET cc_start: 0.8874 (tmm) cc_final: 0.8447 (tmm) REVERT: E 412 GLU cc_start: 0.7014 (tt0) cc_final: 0.6767 (mt-10) REVERT: E 433 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6594 (mmp80) REVERT: E 466 GLU cc_start: 0.7894 (tt0) cc_final: 0.7539 (tt0) REVERT: E 468 TYR cc_start: 0.7851 (m-80) cc_final: 0.7489 (m-80) REVERT: G 12 VAL cc_start: 0.8458 (t) cc_final: 0.7992 (m) REVERT: G 31 ASP cc_start: 0.7740 (p0) cc_final: 0.7383 (p0) REVERT: G 70 PHE cc_start: 0.7496 (m-10) cc_final: 0.7289 (m-10) REVERT: G 109 MET cc_start: 0.7753 (mmm) cc_final: 0.7473 (mmm) REVERT: G 149 GLU cc_start: 0.2253 (mp0) cc_final: 0.1831 (mm-30) REVERT: H 133 MET cc_start: 0.1531 (ppp) cc_final: 0.0440 (tpt) REVERT: I 83 GLU cc_start: 0.7334 (tt0) cc_final: 0.6919 (tt0) REVERT: I 115 LYS cc_start: 0.8275 (ttpp) cc_final: 0.7811 (ttmm) REVERT: I 217 ARG cc_start: 0.7223 (mtt90) cc_final: 0.6828 (mtt90) REVERT: I 308 LYS cc_start: 0.8568 (mtpp) cc_final: 0.8366 (mttp) REVERT: I 324 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7497 (pt) REVERT: I 337 ILE cc_start: 0.9156 (mm) cc_final: 0.8760 (mm) REVERT: I 433 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.5945 (mmp-170) REVERT: I 466 GLU cc_start: 0.7815 (tt0) cc_final: 0.7433 (tm-30) REVERT: K 13 GLN cc_start: 0.7296 (mm110) cc_final: 0.7055 (mm110) REVERT: K 31 ASP cc_start: 0.7424 (p0) cc_final: 0.6928 (p0) REVERT: K 78 GLN cc_start: 0.5216 (mp10) cc_final: 0.4850 (pt0) REVERT: K 109 MET cc_start: 0.7428 (mmm) cc_final: 0.7187 (mmm) REVERT: K 110 ASP cc_start: 0.8218 (p0) cc_final: 0.7973 (p0) REVERT: L 134 MET cc_start: 0.2156 (mtp) cc_final: 0.1129 (mtp) outliers start: 45 outliers final: 26 residues processed: 357 average time/residue: 0.1516 time to fit residues: 83.7568 Evaluate side-chains 336 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 305 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 161 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 143 optimal weight: 30.0000 chunk 152 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 224 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 198 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN 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 ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 ASN ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 ASN L 53 ASN L 79 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.180577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.168408 restraints weight = 25451.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.153744 restraints weight = 53504.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.149417 restraints weight = 49882.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.149628 restraints weight = 56583.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.149971 restraints weight = 41649.113| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.098 20604 Z= 0.344 Angle : 0.836 12.146 27930 Z= 0.426 Chirality : 0.052 0.436 3048 Planarity : 0.006 0.059 3567 Dihedral : 6.373 55.552 2723 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 3.37 % Allowed : 16.04 % Favored : 80.59 % 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: -1.73 (0.16), residues: 2472 helix: 0.61 (0.21), residues: 591 sheet: -1.42 (0.21), residues: 546 loop : -1.88 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 260 TYR 0.022 0.003 TYR E 9 PHE 0.021 0.003 PHE I 415 TRP 0.039 0.003 TRP A 150 HIS 0.007 0.002 HIS E 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00801 / 0.34 (20550) covalent geometry : angle 0.80870 / 0.42 (27795) SS BOND : bond 0.00799 / 0.56 ( 27) SS BOND : angle 2.34757 / 1.79 ( 54) hydrogen bonds : bond 0.05520 / 3.80 ( 774) hydrogen bonds : angle 5.77808 / 4.02 ( 2232) link_BETA1-4 : bond 0.01710 / 0.96 ( 12) link_BETA1-4 : angle 3.07427 / 2.27 ( 36) link_NAG-ASN : bond 0.00568 / 0.35 ( 15) link_NAG-ASN : angle 3.98566 / 2.80 ( 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 401 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 328 time to evaluate : 0.692 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: 0.7703 (mmm-85) cc_final: 0.6972 (mtm-85) REVERT: A 337 ILE cc_start: 0.9081 (mm) cc_final: 0.8682 (mm) REVERT: A 349 TYR cc_start: 0.9273 (OUTLIER) cc_final: 0.8523 (m-80) REVERT: A 411 MET cc_start: 0.9102 (tmm) cc_final: 0.8593 (tmm) REVERT: A 433 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6068 (mtt-85) REVERT: C 31 ASP cc_start: 0.7710 (p0) cc_final: 0.7500 (p0) REVERT: C 60 THR cc_start: 0.8944 (m) cc_final: 0.8528 (p) REVERT: C 78 GLN cc_start: 0.6236 (mp10) cc_final: 0.5883 (pt0) REVERT: C 144 LEU cc_start: 0.4396 (tt) cc_final: 0.4030 (mp) REVERT: D 6 GLN cc_start: 0.6404 (OUTLIER) cc_final: 0.5792 (mm110) REVERT: E 115 LYS cc_start: 0.7320 (ttmt) cc_final: 0.7044 (ttmt) REVERT: E 146 ARG cc_start: 0.7326 (mmt-90) cc_final: 0.7043 (mmt-90) REVERT: E 308 LYS cc_start: 0.8652 (mtpp) cc_final: 0.8386 (mttm) REVERT: E 337 ILE cc_start: 0.9265 (mm) cc_final: 0.8966 (mm) REVERT: E 411 MET cc_start: 0.8849 (tmm) cc_final: 0.8569 (tmm) REVERT: E 433 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6184 (tpt-90) REVERT: E 466 GLU cc_start: 0.7825 (tt0) cc_final: 0.7606 (tt0) REVERT: E 468 TYR cc_start: 0.8291 (m-80) cc_final: 0.7579 (m-80) REVERT: G 12 VAL cc_start: 0.8265 (t) cc_final: 0.7911 (m) REVERT: G 31 ASP cc_start: 0.7910 (p0) cc_final: 0.7564 (p0) REVERT: G 33 TYR cc_start: 0.8447 (m-80) cc_final: 0.8193 (m-10) REVERT: G 109 MET cc_start: 0.7798 (mmm) cc_final: 0.7475 (mmm) REVERT: G 144 LEU cc_start: 0.4868 (mp) cc_final: 0.4503 (mt) REVERT: G 149 GLU cc_start: 0.3130 (mp0) cc_final: 0.2385 (mm-30) REVERT: I 43 LEU cc_start: 0.7590 (mm) cc_final: 0.6960 (mt) REVERT: I 115 LYS cc_start: 0.8469 (ttpp) cc_final: 0.8199 (ttpp) REVERT: I 298 LEU cc_start: 0.8849 (mt) cc_final: 0.8633 (mp) REVERT: I 324 ILE cc_start: 0.7782 (mt) cc_final: 0.7324 (pt) REVERT: I 337 ILE cc_start: 0.9134 (mm) cc_final: 0.8889 (mm) REVERT: I 355 ASN cc_start: 0.8709 (t0) cc_final: 0.8500 (t0) REVERT: I 429 MET cc_start: 0.7749 (mtt) cc_final: 0.7411 (mtt) REVERT: I 433 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6655 (tpt170) REVERT: K 31 ASP cc_start: 0.7521 (p0) cc_final: 0.7257 (p0) REVERT: K 109 MET cc_start: 0.8004 (mmm) cc_final: 0.7589 (mmm) REVERT: K 147 MET cc_start: 0.3171 (ptt) cc_final: 0.2956 (ptt) REVERT: K 149 GLU cc_start: 0.4178 (mm-30) cc_final: 0.3958 (mm-30) REVERT: L 74 LYS cc_start: 0.7333 (mtmm) cc_final: 0.6571 (mtmt) REVERT: L 91 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.7784 (m-10) outliers start: 73 outliers final: 52 residues processed: 379 average time/residue: 0.1497 time to fit residues: 87.9583 Evaluate side-chains 352 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 294 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 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 59 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain D residue 6 GLN 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 176 ILE Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 204 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 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 118 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 204 SER 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: 7.9990 chunk 111 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 154 optimal weight: 10.0000 chunk 160 optimal weight: 20.0000 chunk 169 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 HIS A 477 ASN ** 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 469 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 477 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 = 0.4040 r_free = 0.4040 target = 0.187362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.179893 restraints weight = 25366.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.178741 restraints weight = 47625.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.177913 restraints weight = 54738.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.161120 restraints weight = 51294.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.157703 restraints weight = 51608.767| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20604 Z= 0.178 Angle : 0.682 11.276 27930 Z= 0.347 Chirality : 0.046 0.393 3048 Planarity : 0.005 0.061 3567 Dihedral : 5.926 53.211 2719 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.60 % Allowed : 18.12 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.16), residues: 2472 helix: 0.93 (0.21), residues: 594 sheet: -1.39 (0.21), residues: 561 loop : -1.73 (0.16), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 88 TYR 0.018 0.002 TYR C 82 PHE 0.014 0.002 PHE I 372 TRP 0.029 0.002 TRP A 150 HIS 0.007 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (20550) covalent geometry : angle 0.65573 / 0.34 (27795) SS BOND : bond 0.00507 / 0.36 ( 27) SS BOND : angle 1.80692 / 1.34 ( 54) hydrogen bonds : bond 0.04680 / 3.23 ( 774) hydrogen bonds : angle 5.47187 / 3.81 ( 2232) link_BETA1-4 : bond 0.01315 / 0.75 ( 12) link_BETA1-4 : angle 2.75064 / 2.01 ( 36) link_NAG-ASN : bond 0.00591 / 0.36 ( 15) link_NAG-ASN : angle 3.60668 / 2.56 ( 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: 78 poor density : 320 time to evaluate : 0.749 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: 0.7548 (mmm-85) cc_final: 0.6739 (mtm180) REVERT: A 36 GLU cc_start: 0.7585 (tp30) cc_final: 0.7271 (tp30) REVERT: A 260 ARG cc_start: 0.7526 (tpp-160) cc_final: 0.7251 (tpp-160) REVERT: A 337 ILE cc_start: 0.9022 (mm) cc_final: 0.8634 (mm) REVERT: A 349 TYR cc_start: 0.9270 (OUTLIER) cc_final: 0.8285 (m-80) REVERT: A 411 MET cc_start: 0.9034 (tmm) cc_final: 0.8360 (tmm) REVERT: A 433 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6168 (mtt-85) REVERT: C 6 GLU cc_start: 0.6337 (pt0) cc_final: 0.5950 (pt0) REVERT: C 31 ASP cc_start: 0.7631 (p0) cc_final: 0.7333 (p0) REVERT: C 34 MET cc_start: 0.8081 (tpp) cc_final: 0.7019 (tpp) REVERT: C 60 THR cc_start: 0.8758 (m) cc_final: 0.8421 (p) REVERT: C 144 LEU cc_start: 0.4624 (tt) cc_final: 0.4297 (mp) REVERT: D 69 THR cc_start: 0.7059 (p) cc_final: 0.6730 (p) REVERT: D 74 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.6927 (mmtt) REVERT: D 139 GLU cc_start: 0.4637 (OUTLIER) cc_final: 0.3297 (tp30) REVERT: E 63 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8760 (mm) REVERT: E 115 LYS cc_start: 0.7319 (ttmt) cc_final: 0.6790 (ttmt) REVERT: E 146 ARG cc_start: 0.7474 (mmt-90) cc_final: 0.7157 (mmt-90) REVERT: E 308 LYS cc_start: 0.8651 (mtpp) cc_final: 0.8415 (mttt) REVERT: E 337 ILE cc_start: 0.9180 (mm) cc_final: 0.8973 (mm) REVERT: E 349 TYR cc_start: 0.9084 (OUTLIER) cc_final: 0.8454 (m-80) REVERT: E 433 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.5952 (tpt-90) REVERT: E 466 GLU cc_start: 0.7785 (tt0) cc_final: 0.7508 (tt0) REVERT: E 468 TYR cc_start: 0.8125 (m-80) cc_final: 0.7585 (m-80) REVERT: G 12 VAL cc_start: 0.8237 (t) cc_final: 0.7907 (m) REVERT: G 82 TYR cc_start: 0.6235 (m-80) cc_final: 0.5931 (m-10) REVERT: G 109 MET cc_start: 0.7923 (mmm) cc_final: 0.7579 (mmm) REVERT: G 149 GLU cc_start: 0.3039 (mp0) cc_final: 0.2252 (mm-30) REVERT: I 324 ILE cc_start: 0.7787 (mt) cc_final: 0.7354 (pt) REVERT: I 337 ILE cc_start: 0.9123 (mm) cc_final: 0.8869 (mm) REVERT: I 355 ASN cc_start: 0.8701 (t0) cc_final: 0.8417 (t0) REVERT: I 429 MET cc_start: 0.7648 (mtt) cc_final: 0.7329 (mtt) REVERT: I 433 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.6571 (tpt170) REVERT: I 466 GLU cc_start: 0.7265 (tm-30) cc_final: 0.7050 (tt0) REVERT: I 486 TYR cc_start: 0.8253 (t80) cc_final: 0.7904 (t80) REVERT: K 31 ASP cc_start: 0.7458 (p0) cc_final: 0.7141 (p0) REVERT: K 109 MET cc_start: 0.7916 (mmm) cc_final: 0.7628 (mmm) REVERT: L 74 LYS cc_start: 0.7322 (mtmm) cc_final: 0.6605 (mtmt) REVERT: L 91 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7819 (m-10) outliers start: 78 outliers final: 53 residues processed: 374 average time/residue: 0.1464 time to fit residues: 86.0534 Evaluate side-chains 359 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 297 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL 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 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 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 95 THR Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 139 GLU 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 241 ASN 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 433 ARG Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 95 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 H residue 134 MET Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain I residue 75 VAL 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 241 ASN 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 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 K residue 95 THR Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 91 PHE 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: 8.9990 chunk 81 optimal weight: 8.9990 chunk 168 optimal weight: 0.6980 chunk 149 optimal weight: 10.0000 chunk 201 optimal weight: 0.8980 chunk 146 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 180 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** E 377 ASN E 408 ASN ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.177198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.167468 restraints weight = 25995.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.166314 restraints weight = 48122.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.164575 restraints weight = 52926.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.149230 restraints weight = 71387.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.148557 restraints weight = 57675.925| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 20604 Z= 0.225 Angle : 0.705 11.231 27930 Z= 0.358 Chirality : 0.047 0.400 3048 Planarity : 0.005 0.060 3567 Dihedral : 5.774 44.416 2718 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 4.33 % Allowed : 19.32 % Favored : 76.35 % 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: -1.52 (0.16), residues: 2472 helix: 0.96 (0.21), residues: 594 sheet: -1.50 (0.22), residues: 552 loop : -1.75 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 88 TYR 0.028 0.002 TYR C 82 PHE 0.016 0.002 PHE I 372 TRP 0.033 0.002 TRP A 150 HIS 0.005 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 (20550) covalent geometry : angle 0.67796 / 0.35 (27795) SS BOND : bond 0.00572 / 0.42 ( 27) SS BOND : angle 2.07712 / 1.55 ( 54) hydrogen bonds : bond 0.04771 / 3.29 ( 774) hydrogen bonds : angle 5.40344 / 3.77 ( 2232) link_BETA1-4 : bond 0.01370 / 0.79 ( 12) link_BETA1-4 : angle 2.77822 / 2.04 ( 36) link_NAG-ASN : bond 0.00548 / 0.34 ( 15) link_NAG-ASN : angle 3.64104 / 2.58 ( 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 405 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 311 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7663 (mmm-85) cc_final: 0.6865 (mtm180) REVERT: A 36 GLU cc_start: 0.7498 (tp30) cc_final: 0.7186 (tp30) REVERT: A 63 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8255 (mm) REVERT: A 337 ILE cc_start: 0.8862 (mm) cc_final: 0.8481 (mm) REVERT: A 349 TYR cc_start: 0.9277 (OUTLIER) cc_final: 0.8369 (m-80) REVERT: A 411 MET cc_start: 0.8908 (tmm) cc_final: 0.8210 (tmm) REVERT: A 433 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6392 (mtt-85) REVERT: C 31 ASP cc_start: 0.7646 (p0) cc_final: 0.7438 (p0) REVERT: C 60 THR cc_start: 0.8890 (m) cc_final: 0.8427 (p) REVERT: C 144 LEU cc_start: 0.4817 (tt) cc_final: 0.4501 (mp) REVERT: D 69 THR cc_start: 0.7058 (p) cc_final: 0.6769 (p) REVERT: D 139 GLU cc_start: 0.4687 (OUTLIER) cc_final: 0.3282 (tp30) REVERT: E 63 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8678 (mm) REVERT: E 115 LYS cc_start: 0.7343 (ttmt) cc_final: 0.6655 (ttmt) REVERT: E 146 ARG cc_start: 0.7302 (mmt-90) cc_final: 0.7082 (mmt-90) REVERT: E 213 GLU cc_start: 0.7699 (pm20) cc_final: 0.6863 (pm20) REVERT: E 308 LYS cc_start: 0.8690 (mtpp) cc_final: 0.8387 (mttt) REVERT: E 349 TYR cc_start: 0.9110 (OUTLIER) cc_final: 0.8356 (m-80) REVERT: E 433 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.5982 (tpt-90) REVERT: E 468 TYR cc_start: 0.8181 (m-80) cc_final: 0.7595 (m-80) REVERT: G 12 VAL cc_start: 0.8265 (t) cc_final: 0.7968 (m) REVERT: G 109 MET cc_start: 0.8002 (mmm) cc_final: 0.7663 (mmm) REVERT: G 149 GLU cc_start: 0.3193 (mp0) cc_final: 0.2479 (mm-30) REVERT: I 43 LEU cc_start: 0.7333 (mm) cc_final: 0.6775 (mt) REVERT: I 324 ILE cc_start: 0.7660 (mt) cc_final: 0.7194 (pt) REVERT: I 337 ILE cc_start: 0.9119 (mm) cc_final: 0.8859 (mm) REVERT: I 355 ASN cc_start: 0.8755 (t0) cc_final: 0.8446 (t0) REVERT: I 425 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8611 (tt) REVERT: I 429 MET cc_start: 0.7746 (mtt) cc_final: 0.7427 (mtt) REVERT: I 433 ARG cc_start: 0.7111 (tpp80) cc_final: 0.6779 (tpt170) REVERT: I 486 TYR cc_start: 0.8256 (t80) cc_final: 0.7710 (t80) REVERT: K 13 GLN cc_start: 0.7082 (mm110) cc_final: 0.6826 (mm110) REVERT: K 31 ASP cc_start: 0.7473 (p0) cc_final: 0.7033 (p0) REVERT: L 74 LYS cc_start: 0.7194 (mtmm) cc_final: 0.6396 (mtmt) outliers start: 94 outliers final: 67 residues processed: 380 average time/residue: 0.1444 time to fit residues: 85.9052 Evaluate side-chains 361 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 286 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 118 ILE Chi-restraints excluded: chain A residue 149 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 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 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 95 THR 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 D residue 139 GLU 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 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 433 ARG 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 37 VAL 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 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 134 MET Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain I residue 5 ILE 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 241 ASN 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 I residue 425 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 145 optimal weight: 30.0000 chunk 57 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 13 optimal weight: 0.0170 chunk 191 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 211 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 overall best weight: 2.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** ** 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 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.187075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.180307 restraints weight = 25208.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.179662 restraints weight = 35405.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.178267 restraints weight = 46828.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.161821 restraints weight = 40853.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.158698 restraints weight = 51828.288| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20604 Z= 0.169 Angle : 0.663 10.879 27930 Z= 0.336 Chirality : 0.046 0.386 3048 Planarity : 0.005 0.061 3567 Dihedral : 5.441 40.062 2710 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.73 % Allowed : 21.39 % Favored : 74.87 % 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: -1.41 (0.17), residues: 2472 helix: 1.05 (0.21), residues: 600 sheet: -1.42 (0.22), residues: 549 loop : -1.68 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 126 TYR 0.023 0.002 TYR C 82 PHE 0.014 0.002 PHE I 372 TRP 0.027 0.001 TRP I 150 HIS 0.010 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (20550) covalent geometry : angle 0.63753 / 0.33 (27795) SS BOND : bond 0.00468 / 0.33 ( 27) SS BOND : angle 1.84365 / 1.36 ( 54) hydrogen bonds : bond 0.04496 / 3.09 ( 774) hydrogen bonds : angle 5.29824 / 3.70 ( 2232) link_BETA1-4 : bond 0.01291 / 0.75 ( 12) link_BETA1-4 : angle 2.65555 / 1.95 ( 36) link_NAG-ASN : bond 0.00581 / 0.36 ( 15) link_NAG-ASN : angle 3.49206 / 2.48 ( 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 383 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 302 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7649 (mmm-85) cc_final: 0.6819 (mtm180) REVERT: A 337 ILE cc_start: 0.9046 (mm) cc_final: 0.8641 (mm) REVERT: A 349 TYR cc_start: 0.9293 (OUTLIER) cc_final: 0.8345 (m-80) REVERT: A 411 MET cc_start: 0.8875 (tmm) cc_final: 0.8231 (tmm) REVERT: A 433 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6313 (mtt-85) REVERT: C 31 ASP cc_start: 0.7683 (p0) cc_final: 0.7407 (p0) REVERT: C 34 MET cc_start: 0.8128 (tpp) cc_final: 0.7354 (tpp) REVERT: C 60 THR cc_start: 0.8800 (m) cc_final: 0.8358 (p) REVERT: C 144 LEU cc_start: 0.4975 (tt) cc_final: 0.4673 (mp) REVERT: D 69 THR cc_start: 0.6854 (p) cc_final: 0.6550 (p) REVERT: D 139 GLU cc_start: 0.4273 (OUTLIER) cc_final: 0.3188 (tp30) REVERT: E 308 LYS cc_start: 0.8683 (mtpp) cc_final: 0.8403 (mttt) REVERT: E 349 TYR cc_start: 0.9115 (OUTLIER) cc_final: 0.8331 (m-80) REVERT: E 433 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.5732 (tpt-90) REVERT: E 468 TYR cc_start: 0.8108 (m-80) cc_final: 0.7544 (m-80) REVERT: G 12 VAL cc_start: 0.8280 (t) cc_final: 0.8013 (m) REVERT: G 109 MET cc_start: 0.8029 (mmm) cc_final: 0.7670 (mmm) REVERT: G 149 GLU cc_start: 0.3095 (mp0) cc_final: 0.2197 (mm-30) REVERT: I 324 ILE cc_start: 0.7636 (mt) cc_final: 0.7215 (pt) REVERT: I 337 ILE cc_start: 0.9115 (mm) cc_final: 0.8854 (mm) REVERT: I 355 ASN cc_start: 0.8726 (t0) cc_final: 0.8397 (t0) REVERT: I 429 MET cc_start: 0.7661 (mtt) cc_final: 0.7321 (mtt) REVERT: I 433 ARG cc_start: 0.7038 (tpp80) cc_final: 0.6614 (tpt-90) REVERT: K 31 ASP cc_start: 0.7430 (p0) cc_final: 0.7003 (p0) REVERT: L 74 LYS cc_start: 0.6853 (mtmm) cc_final: 0.5983 (mtmt) outliers start: 81 outliers final: 61 residues processed: 358 average time/residue: 0.1442 time to fit residues: 81.1153 Evaluate side-chains 353 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 287 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 110 VAL 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 D residue 15 VAL Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 139 GLU 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 349 TYR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain E residue 475 CYS Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 37 VAL 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 H residue 134 MET Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain I residue 5 ILE 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 241 ASN 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 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 80 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 27 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 239 optimal weight: 20.0000 chunk 182 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 64 optimal weight: 20.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN ** 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 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 ASN ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.179898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.170275 restraints weight = 25945.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.169725 restraints weight = 44513.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.168237 restraints weight = 46214.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.167274 restraints weight = 58539.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.166857 restraints weight = 56139.038| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20604 Z= 0.156 Angle : 0.650 10.532 27930 Z= 0.328 Chirality : 0.046 0.383 3048 Planarity : 0.004 0.061 3567 Dihedral : 5.284 40.300 2709 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.92 % Allowed : 21.58 % Favored : 74.50 % 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: -1.28 (0.17), residues: 2472 helix: 1.16 (0.21), residues: 600 sheet: -1.35 (0.22), residues: 549 loop : -1.60 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 260 TYR 0.032 0.002 TYR C 82 PHE 0.012 0.001 PHE A 372 TRP 0.027 0.001 TRP I 150 HIS 0.003 0.001 HIS I 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (20550) covalent geometry : angle 0.62489 / 0.32 (27795) SS BOND : bond 0.00447 / 0.31 ( 27) SS BOND : angle 1.85216 / 1.36 ( 54) hydrogen bonds : bond 0.04354 / 3.00 ( 774) hydrogen bonds : angle 5.15536 / 3.61 ( 2232) link_BETA1-4 : bond 0.01261 / 0.72 ( 12) link_BETA1-4 : angle 2.58602 / 1.90 ( 36) link_NAG-ASN : bond 0.00600 / 0.37 ( 15) link_NAG-ASN : angle 3.36707 / 2.40 ( 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 390 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 305 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7658 (mmm-85) cc_final: 0.6798 (mtm-85) REVERT: A 129 THR cc_start: 0.8221 (m) cc_final: 0.7812 (m) REVERT: A 337 ILE cc_start: 0.9034 (mm) cc_final: 0.8657 (mm) REVERT: A 349 TYR cc_start: 0.9289 (OUTLIER) cc_final: 0.8373 (m-80) REVERT: A 411 MET cc_start: 0.9104 (tmm) cc_final: 0.8510 (tmm) REVERT: A 433 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6153 (mpt180) REVERT: C 31 ASP cc_start: 0.7585 (p0) cc_final: 0.7347 (p0) REVERT: C 34 MET cc_start: 0.8032 (tpp) cc_final: 0.7264 (tpp) REVERT: C 60 THR cc_start: 0.8711 (m) cc_final: 0.8253 (p) REVERT: D 69 THR cc_start: 0.6509 (p) cc_final: 0.6209 (p) REVERT: D 139 GLU cc_start: 0.3735 (OUTLIER) cc_final: 0.3376 (tp30) REVERT: E 146 ARG cc_start: 0.7119 (mmt-90) cc_final: 0.6856 (mmt-90) REVERT: E 162 LYS cc_start: 0.6981 (tppp) cc_final: 0.6628 (tptp) REVERT: E 213 GLU cc_start: 0.7537 (pm20) cc_final: 0.6980 (pm20) REVERT: E 247 ASN cc_start: 0.8533 (m110) cc_final: 0.8000 (m-40) REVERT: E 265 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8518 (mt) REVERT: E 308 LYS cc_start: 0.8711 (mtpp) cc_final: 0.8465 (mttt) REVERT: E 349 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.8320 (m-80) REVERT: E 366 GLU cc_start: 0.6649 (tt0) cc_final: 0.6339 (tt0) REVERT: E 433 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.6414 (mmp80) REVERT: E 468 TYR cc_start: 0.8021 (m-80) cc_final: 0.7287 (m-80) REVERT: G 109 MET cc_start: 0.7997 (mmm) cc_final: 0.7552 (mmm) REVERT: G 149 GLU cc_start: 0.2839 (mp0) cc_final: 0.1993 (mm-30) REVERT: I 36 GLU cc_start: 0.7952 (tp30) cc_final: 0.7600 (tp30) REVERT: I 213 GLU cc_start: 0.8052 (pm20) cc_final: 0.7530 (pm20) REVERT: I 324 ILE cc_start: 0.7556 (mt) cc_final: 0.7306 (pt) REVERT: I 337 ILE cc_start: 0.9077 (mm) cc_final: 0.8857 (mm) REVERT: I 355 ASN cc_start: 0.8601 (t0) cc_final: 0.8245 (t0) REVERT: I 429 MET cc_start: 0.7629 (mtt) cc_final: 0.7123 (mtt) REVERT: I 433 ARG cc_start: 0.7038 (tpp80) cc_final: 0.6314 (mmp-170) REVERT: K 31 ASP cc_start: 0.7399 (p0) cc_final: 0.7038 (p0) REVERT: K 144 LEU cc_start: 0.5485 (mp) cc_final: 0.5265 (tt) REVERT: L 74 LYS cc_start: 0.6681 (mtmm) cc_final: 0.5990 (mtmt) outliers start: 85 outliers final: 66 residues processed: 363 average time/residue: 0.1412 time to fit residues: 80.4787 Evaluate side-chains 359 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 287 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL 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 95 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 139 GLU 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 202 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 252 GLU 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 433 ARG Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 164 GLN 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 134 MET Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 241 ASN 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 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 80 ILE 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: 3.9990 chunk 39 optimal weight: 7.9990 chunk 96 optimal weight: 0.5980 chunk 153 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 198 optimal weight: 0.6980 chunk 186 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 146 optimal weight: 30.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 377 ASN ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** 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 = 0.3965 r_free = 0.3965 target = 0.179893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.169655 restraints weight = 25880.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.167277 restraints weight = 47404.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.166611 restraints weight = 67103.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.154245 restraints weight = 55159.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.150815 restraints weight = 53942.999| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20604 Z= 0.184 Angle : 0.668 10.764 27930 Z= 0.336 Chirality : 0.046 0.391 3048 Planarity : 0.005 0.061 3567 Dihedral : 5.313 39.838 2709 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.87 % Allowed : 21.25 % Favored : 74.87 % 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: -1.32 (0.17), residues: 2472 helix: 1.15 (0.21), residues: 600 sheet: -1.33 (0.23), residues: 516 loop : -1.67 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 19 TYR 0.026 0.002 TYR C 82 PHE 0.014 0.002 PHE I 372 TRP 0.029 0.002 TRP I 150 HIS 0.005 0.001 HIS E 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (20550) covalent geometry : angle 0.64531 / 0.33 (27795) SS BOND : bond 0.00684 / 0.51 ( 27) SS BOND : angle 1.56795 / 1.17 ( 54) hydrogen bonds : bond 0.04450 / 3.06 ( 774) hydrogen bonds : angle 5.18275 / 3.63 ( 2232) link_BETA1-4 : bond 0.01275 / 0.74 ( 12) link_BETA1-4 : angle 2.59471 / 1.91 ( 36) link_NAG-ASN : bond 0.00576 / 0.35 ( 15) link_NAG-ASN : angle 3.40855 / 2.43 ( 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 386 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 302 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7604 (mmm-85) cc_final: 0.6797 (mtm-85) REVERT: A 63 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8266 (mm) REVERT: A 337 ILE cc_start: 0.9063 (mm) cc_final: 0.8661 (mm) REVERT: A 349 TYR cc_start: 0.9293 (OUTLIER) cc_final: 0.8438 (m-80) REVERT: A 411 MET cc_start: 0.8961 (tmm) cc_final: 0.8388 (tmm) REVERT: A 433 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.6946 (mtt-85) REVERT: C 31 ASP cc_start: 0.7830 (p0) cc_final: 0.7552 (p0) REVERT: C 34 MET cc_start: 0.8177 (tpp) cc_final: 0.7387 (tpp) REVERT: C 60 THR cc_start: 0.8766 (m) cc_final: 0.8316 (p) REVERT: D 69 THR cc_start: 0.6930 (p) cc_final: 0.6621 (p) REVERT: D 139 GLU cc_start: 0.5387 (OUTLIER) cc_final: 0.4128 (tp30) REVERT: E 162 LYS cc_start: 0.7042 (tppp) cc_final: 0.6617 (tptp) REVERT: E 247 ASN cc_start: 0.8566 (m110) cc_final: 0.8071 (m-40) REVERT: E 256 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7993 (tptt) REVERT: E 265 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8584 (mt) REVERT: E 308 LYS cc_start: 0.8719 (mtpp) cc_final: 0.8493 (mttt) REVERT: E 337 ILE cc_start: 0.9062 (mm) cc_final: 0.8607 (mm) REVERT: E 349 TYR cc_start: 0.9076 (OUTLIER) cc_final: 0.8145 (m-80) REVERT: E 366 GLU cc_start: 0.6785 (tt0) cc_final: 0.6521 (tt0) REVERT: G 109 MET cc_start: 0.8238 (mmm) cc_final: 0.7845 (mmm) REVERT: G 149 GLU cc_start: 0.3154 (mp0) cc_final: 0.2230 (mm-30) REVERT: H 74 LYS cc_start: 0.6783 (mtmm) cc_final: 0.6559 (mtmm) REVERT: I 36 GLU cc_start: 0.7945 (tp30) cc_final: 0.7607 (tp30) REVERT: I 337 ILE cc_start: 0.9158 (mm) cc_final: 0.8935 (mm) REVERT: I 355 ASN cc_start: 0.8588 (t0) cc_final: 0.8216 (t0) REVERT: I 386 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7581 (tt) REVERT: I 429 MET cc_start: 0.7803 (mtt) cc_final: 0.7416 (mtt) REVERT: I 433 ARG cc_start: 0.6887 (tpp80) cc_final: 0.6449 (mmp-170) REVERT: K 31 ASP cc_start: 0.7523 (p0) cc_final: 0.7113 (p0) REVERT: K 144 LEU cc_start: 0.5013 (mp) cc_final: 0.4724 (tt) REVERT: L 74 LYS cc_start: 0.6859 (mtmm) cc_final: 0.6056 (mtmt) REVERT: L 134 MET cc_start: 0.2566 (mtp) cc_final: 0.1964 (mtp) outliers start: 84 outliers final: 68 residues processed: 362 average time/residue: 0.1369 time to fit residues: 78.1219 Evaluate side-chains 365 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 289 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 266 ILE 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 95 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 139 GLU 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 202 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 256 LYS 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 386 ILE 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 22 CYS Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 164 GLN 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 134 MET Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain I residue 5 ILE 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 241 ASN 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 386 ILE 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: 5.9990 chunk 209 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 chunk 146 optimal weight: 30.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** 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 = 0.4025 r_free = 0.4025 target = 0.185638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.178504 restraints weight = 25376.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.176664 restraints weight = 46176.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.175259 restraints weight = 61148.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.162102 restraints weight = 52037.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.158275 restraints weight = 44658.423| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20604 Z= 0.190 Angle : 0.679 10.823 27930 Z= 0.343 Chirality : 0.046 0.392 3048 Planarity : 0.005 0.063 3567 Dihedral : 5.269 39.039 2705 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.92 % Allowed : 21.53 % Favored : 74.55 % 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: -1.33 (0.17), residues: 2472 helix: 1.13 (0.21), residues: 600 sheet: -1.34 (0.23), residues: 516 loop : -1.66 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 149 TYR 0.028 0.002 TYR E 80 PHE 0.015 0.002 PHE I 372 TRP 0.031 0.002 TRP I 150 HIS 0.008 0.001 HIS E 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (20550) covalent geometry : angle 0.65548 / 0.34 (27795) SS BOND : bond 0.00678 / 0.50 ( 27) SS BOND : angle 1.73945 / 1.25 ( 54) hydrogen bonds : bond 0.04483 / 3.07 ( 774) hydrogen bonds : angle 5.17755 / 3.62 ( 2232) link_BETA1-4 : bond 0.01262 / 0.72 ( 12) link_BETA1-4 : angle 2.56018 / 1.88 ( 36) link_NAG-ASN : bond 0.00570 / 0.35 ( 15) link_NAG-ASN : angle 3.42290 / 2.44 ( 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 379 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 294 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7633 (mmm-85) cc_final: 0.6833 (mtm-85) REVERT: A 63 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8322 (mm) REVERT: A 337 ILE cc_start: 0.9074 (mm) cc_final: 0.8657 (mm) REVERT: A 349 TYR cc_start: 0.9285 (OUTLIER) cc_final: 0.8479 (m-80) REVERT: A 366 GLU cc_start: 0.6928 (tt0) cc_final: 0.6608 (tt0) REVERT: A 411 MET cc_start: 0.8986 (tmm) cc_final: 0.8404 (tmm) REVERT: C 31 ASP cc_start: 0.7804 (p0) cc_final: 0.7558 (p0) REVERT: C 34 MET cc_start: 0.8123 (tpp) cc_final: 0.7268 (tpp) REVERT: C 60 THR cc_start: 0.8783 (m) cc_final: 0.8278 (p) REVERT: D 69 THR cc_start: 0.6890 (p) cc_final: 0.6640 (p) REVERT: D 139 GLU cc_start: 0.5287 (OUTLIER) cc_final: 0.4094 (tp30) REVERT: E 146 ARG cc_start: 0.6587 (mmt-90) cc_final: 0.6310 (mmt-90) REVERT: E 162 LYS cc_start: 0.7041 (tppp) cc_final: 0.6628 (tptp) REVERT: E 247 ASN cc_start: 0.8720 (m110) cc_final: 0.8251 (m-40) REVERT: E 265 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8595 (mt) REVERT: E 308 LYS cc_start: 0.8726 (mtpp) cc_final: 0.8516 (mttt) REVERT: E 337 ILE cc_start: 0.9182 (mm) cc_final: 0.8718 (mm) REVERT: E 355 ASN cc_start: 0.8672 (t0) cc_final: 0.8438 (t0) REVERT: E 366 GLU cc_start: 0.6777 (tt0) cc_final: 0.6554 (tt0) REVERT: G 149 GLU cc_start: 0.3155 (mp0) cc_final: 0.2118 (mm-30) REVERT: I 36 GLU cc_start: 0.7953 (tp30) cc_final: 0.7622 (tp30) REVERT: I 213 GLU cc_start: 0.8225 (pm20) cc_final: 0.7617 (pm20) REVERT: I 337 ILE cc_start: 0.9159 (mm) cc_final: 0.8949 (mm) REVERT: I 355 ASN cc_start: 0.8620 (t0) cc_final: 0.8228 (t0) REVERT: I 386 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7763 (tt) REVERT: I 429 MET cc_start: 0.7744 (mtt) cc_final: 0.7495 (mtt) REVERT: K 31 ASP cc_start: 0.7504 (p0) cc_final: 0.7075 (p0) REVERT: L 74 LYS cc_start: 0.6854 (mtmm) cc_final: 0.6069 (mtmt) REVERT: L 134 MET cc_start: 0.2707 (mtp) cc_final: 0.2114 (mtp) outliers start: 85 outliers final: 73 residues processed: 357 average time/residue: 0.1316 time to fit residues: 74.5880 Evaluate side-chains 362 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 284 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 202 SER 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 266 ILE 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 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 95 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 157 GLU 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 202 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 252 GLU 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 475 CYS Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 147 MET Chi-restraints excluded: chain G residue 164 GLN 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 H residue 134 MET Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain I residue 5 ILE 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 241 ASN 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 386 ILE 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 109 MET Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 237 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 29 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 232 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 214 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 207 ASN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.173791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.159931 restraints weight = 25529.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.158131 restraints weight = 45714.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.157080 restraints weight = 60522.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.156148 restraints weight = 52047.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.155657 restraints weight = 56336.693| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20604 Z= 0.170 Angle : 0.665 10.708 27930 Z= 0.336 Chirality : 0.046 0.389 3048 Planarity : 0.005 0.065 3567 Dihedral : 5.212 39.126 2705 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.69 % Allowed : 21.85 % Favored : 74.46 % 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: -1.28 (0.17), residues: 2472 helix: 1.18 (0.21), residues: 600 sheet: -1.34 (0.23), residues: 516 loop : -1.62 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 74 TYR 0.025 0.002 TYR I 468 PHE 0.017 0.002 PHE G 70 TRP 0.031 0.001 TRP A 150 HIS 0.007 0.001 HIS E 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (20550) covalent geometry : angle 0.64258 / 0.33 (27795) SS BOND : bond 0.00635 / 0.46 ( 27) SS BOND : angle 1.49951 / 1.11 ( 54) hydrogen bonds : bond 0.04362 / 2.99 ( 774) hydrogen bonds : angle 5.15623 / 3.61 ( 2232) link_BETA1-4 : bond 0.01245 / 0.72 ( 12) link_BETA1-4 : angle 2.51077 / 1.85 ( 36) link_NAG-ASN : bond 0.00588 / 0.36 ( 15) link_NAG-ASN : angle 3.37022 / 2.41 ( 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 377 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 297 time to evaluate : 0.731 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: 0.7603 (mmm-85) cc_final: 0.6796 (mtm-85) REVERT: A 63 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8227 (mm) REVERT: A 337 ILE cc_start: 0.9061 (mm) cc_final: 0.8644 (mm) REVERT: A 349 TYR cc_start: 0.9300 (OUTLIER) cc_final: 0.8475 (m-80) REVERT: A 366 GLU cc_start: 0.6910 (tt0) cc_final: 0.6479 (tt0) REVERT: A 411 MET cc_start: 0.8959 (tmm) cc_final: 0.8403 (tmm) REVERT: A 433 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6958 (tpt170) REVERT: A 476 MET cc_start: 0.8183 (ttm) cc_final: 0.7898 (ttm) REVERT: C 31 ASP cc_start: 0.7870 (p0) cc_final: 0.7594 (p0) REVERT: C 34 MET cc_start: 0.8092 (tpp) cc_final: 0.7158 (tpp) REVERT: C 60 THR cc_start: 0.8722 (m) cc_final: 0.8273 (p) REVERT: D 69 THR cc_start: 0.6582 (p) cc_final: 0.6252 (p) REVERT: D 139 GLU cc_start: 0.3784 (OUTLIER) cc_final: 0.3518 (tp30) REVERT: E 162 LYS cc_start: 0.6938 (tppp) cc_final: 0.6594 (tptp) REVERT: E 247 ASN cc_start: 0.8687 (m110) cc_final: 0.8239 (m-40) REVERT: E 265 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8559 (mt) REVERT: E 308 LYS cc_start: 0.8700 (mtpp) cc_final: 0.8499 (mttt) REVERT: E 337 ILE cc_start: 0.9159 (mm) cc_final: 0.8701 (mm) REVERT: E 355 ASN cc_start: 0.8596 (t0) cc_final: 0.8324 (t0) REVERT: E 366 GLU cc_start: 0.6767 (tt0) cc_final: 0.6539 (tt0) REVERT: G 109 MET cc_start: 0.8043 (mmm) cc_final: 0.7722 (mmm) REVERT: G 149 GLU cc_start: 0.2983 (mp0) cc_final: 0.1889 (mm-30) REVERT: I 36 GLU cc_start: 0.7894 (tp30) cc_final: 0.7536 (tp30) REVERT: I 213 GLU cc_start: 0.8128 (pm20) cc_final: 0.7543 (pm20) REVERT: I 337 ILE cc_start: 0.9122 (mm) cc_final: 0.8894 (mm) REVERT: I 355 ASN cc_start: 0.8613 (t0) cc_final: 0.8209 (t0) REVERT: K 31 ASP cc_start: 0.7509 (p0) cc_final: 0.7091 (p0) REVERT: L 12 SER cc_start: 0.6970 (t) cc_final: 0.6705 (p) REVERT: L 74 LYS cc_start: 0.6511 (mtmm) cc_final: 0.5812 (mtmt) REVERT: L 134 MET cc_start: 0.3416 (mtp) cc_final: 0.2958 (mtp) outliers start: 80 outliers final: 66 residues processed: 356 average time/residue: 0.1329 time to fit residues: 75.1740 Evaluate side-chains 359 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 288 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 202 SER 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 266 ILE 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 59 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 ASP 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 D residue 139 GLU Chi-restraints excluded: chain D residue 157 GLU 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 202 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 252 GLU 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 475 CYS Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain G residue 22 CYS 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 147 MET Chi-restraints excluded: chain G residue 164 GLN 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 H residue 134 MET Chi-restraints excluded: chain H residue 135 GLU 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 241 ASN 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 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 32 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 240 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 19 optimal weight: 0.2980 chunk 204 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 212 optimal weight: 20.0000 chunk 31 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 228 optimal weight: 6.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 241 ASN E 377 ASN ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 ASN K 78 GLN ** 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 = 0.3977 r_free = 0.3977 target = 0.180990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.170683 restraints weight = 26045.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.168812 restraints weight = 46105.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.167981 restraints weight = 60119.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.166992 restraints weight = 60645.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.166670 restraints weight = 65380.469| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20604 Z= 0.133 Angle : 0.639 10.318 27930 Z= 0.322 Chirality : 0.045 0.376 3048 Planarity : 0.005 0.064 3567 Dihedral : 5.040 36.152 2705 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.86 % Allowed : 22.45 % Favored : 74.69 % 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: -1.20 (0.17), residues: 2472 helix: 1.25 (0.21), residues: 597 sheet: -1.30 (0.23), residues: 516 loop : -1.56 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 74 TYR 0.023 0.002 TYR G 82 PHE 0.014 0.001 PHE A 372 TRP 0.022 0.001 TRP I 150 HIS 0.006 0.001 HIS E 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (20550) covalent geometry : angle 0.61871 / 0.32 (27795) SS BOND : bond 0.00493 / 0.36 ( 27) SS BOND : angle 1.28340 / 0.93 ( 54) hydrogen bonds : bond 0.04120 / 2.82 ( 774) hydrogen bonds : angle 5.04438 / 3.52 ( 2232) link_BETA1-4 : bond 0.01177 / 0.68 ( 12) link_BETA1-4 : angle 2.42814 / 1.79 ( 36) link_NAG-ASN : bond 0.00626 / 0.38 ( 15) link_NAG-ASN : angle 3.20638 / 2.30 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3134.41 seconds wall clock time: 55 minutes 34.36 seconds (3334.36 seconds total)