Starting phenix.real_space_refine on Wed Mar 4 15:36:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yhk_33831/03_2026/7yhk_33831.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yhk_33831/03_2026/7yhk_33831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yhk_33831/03_2026/7yhk_33831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yhk_33831/03_2026/7yhk_33831.map" model { file = "/net/cci-nas-00/data/ceres_data/7yhk_33831/03_2026/7yhk_33831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yhk_33831/03_2026/7yhk_33831.cif" } resolution = 3.14 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= 0.025 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 60 5.16 5 C 9153 2.51 5 N 2439 2.21 5 O 2850 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14502 Number of models: 1 Model: "" Number of chains: 5 Chain: "F" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 906 Classifications: {'peptide': 116} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 110} Chain: "H" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 847 Classifications: {'peptide': 111} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 4, 'TRANS': 102} Chain: "A" Number of atoms: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2997 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 18, 'TRANS': 358} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: C, I, D, J, E, K, G, L Time building chain proxies: 2.93, per 1000 atoms: 0.20 Number of scatterers: 14502 At special positions: 0 Unit cell: (142.374, 147.042, 124.48, 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 60 16.00 O 2850 8.00 N 2439 7.00 C 9153 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 278 " distance=2.03 Simple disulfide: pdb=" SG CYS K 46 " - pdb=" SG CYS K 278 " distance=2.03 Simple disulfide: pdb=" SG CYS E 59 " - pdb=" SG CYS E 71 " distance=2.03 Simple disulfide: pdb=" SG CYS K 59 " - pdb=" SG CYS K 71 " distance=2.03 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS K 94 " - pdb=" SG CYS K 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 282 " - pdb=" SG CYS E 306 " distance=2.02 Simple disulfide: pdb=" SG CYS K 282 " - pdb=" SG CYS K 306 " distance=2.02 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 G 1 " - " NAG G 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A 601 " - " ASN A 58 " " NAG A 602 " - " ASN A 27 " " NAG A 603 " - " ASN A 163 " " NAG A 604 " - " ASN A 290 " " NAG B 1 " - " ASN A 91 " " NAG E 601 " - " ASN E 58 " " NAG E 602 " - " ASN E 27 " " NAG E 603 " - " ASN E 163 " " NAG E 604 " - " ASN E 290 " " NAG G 1 " - " ASN E 91 " " NAG K 601 " - " ASN K 58 " " NAG K 602 " - " ASN K 27 " " NAG K 603 " - " ASN K 163 " " NAG K 604 " - " ASN K 290 " " NAG L 1 " - " ASN K 91 " Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 608.8 milliseconds 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3354 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 45 sheets defined 14.6% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'F' and resid 62 through 65 removed outlier: 3.519A pdb=" N LYS F 65 " --> pdb=" O ASP F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.727A pdb=" N ASP H 86 " --> pdb=" O GLU H 83 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA H 87 " --> pdb=" O GLU H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 71 through 75 removed outlier: 3.749A pdb=" N LEU A 74 " --> pdb=" O CYS A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 109 removed outlier: 3.586A pdb=" N GLU A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.522A pdb=" N GLN A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.961A pdb=" N LYS A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASN A 390 " --> pdb=" O ILE A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 442 removed outlier: 3.504A pdb=" N ASP A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.608A pdb=" N ASN A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.520A pdb=" N LYS C 65 " --> pdb=" O ASP C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.728A pdb=" N ASP D 86 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA D 87 " --> pdb=" O GLU D 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 83 through 87' Processing helix chain 'E' and resid 61 through 66 Processing helix chain 'E' and resid 71 through 75 removed outlier: 3.748A pdb=" N LEU E 74 " --> pdb=" O CYS E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 109 removed outlier: 3.586A pdb=" N GLU E 107 " --> pdb=" O GLU E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 195 removed outlier: 3.522A pdb=" N GLN E 191 " --> pdb=" O ASN E 187 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA E 193 " --> pdb=" O GLY E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 390 removed outlier: 3.961A pdb=" N LYS E 388 " --> pdb=" O SER E 384 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASN E 390 " --> pdb=" O ILE E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 442 removed outlier: 3.505A pdb=" N ASP E 420 " --> pdb=" O ASP E 416 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR E 423 " --> pdb=" O LEU E 419 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU E 435 " --> pdb=" O LEU E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 448 removed outlier: 3.608A pdb=" N ASN E 447 " --> pdb=" O SER E 443 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 65 removed outlier: 3.518A pdb=" N LYS I 65 " --> pdb=" O ASP I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.726A pdb=" N ASP J 86 " --> pdb=" O GLU J 83 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA J 87 " --> pdb=" O GLU J 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 83 through 87' Processing helix chain 'K' and resid 61 through 66 Processing helix chain 'K' and resid 71 through 75 removed outlier: 3.749A pdb=" N LEU K 74 " --> pdb=" O CYS K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 109 removed outlier: 3.586A pdb=" N GLU K 107 " --> pdb=" O GLU K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 195 removed outlier: 3.523A pdb=" N GLN K 191 " --> pdb=" O ASN K 187 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA K 193 " --> pdb=" O GLY K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 390 removed outlier: 3.962A pdb=" N LYS K 388 " --> pdb=" O SER K 384 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASN K 390 " --> pdb=" O ILE K 386 " (cutoff:3.500A) Processing helix chain 'K' and resid 407 through 442 removed outlier: 3.504A pdb=" N ASP K 420 " --> pdb=" O ASP K 416 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR K 423 " --> pdb=" O LEU K 419 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU K 435 " --> pdb=" O LEU K 431 " (cutoff:3.500A) Processing helix chain 'K' and resid 443 through 448 removed outlier: 3.608A pdb=" N ASN K 447 " --> pdb=" O SER K 443 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.760A pdb=" N VAL F 18 " --> pdb=" O ILE F 83 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.275A pdb=" N GLU F 10 " --> pdb=" O THR F 114 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TRP F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA F 40 " --> pdb=" O GLY F 44 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.732A pdb=" N ASP H 74 " --> pdb=" O SER H 71 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.870A pdb=" N GLU H 109 " --> pdb=" O LEU H 11 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'H' and resid 30 through 31 Processing sheet with id=6, first strand: chain 'H' and resid 57 through 58 removed outlier: 3.569A pdb=" N ASN H 57 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU H 50 " --> pdb=" O GLN H 41 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLN H 41 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR H 101 " --> pdb=" O GLN H 94 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=8, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=9, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=10, first strand: chain 'A' and resid 54 through 57 removed outlier: 6.839A pdb=" N LEU A 54 " --> pdb=" O VAL A 84 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'A' and resid 112 through 114 removed outlier: 6.983A pdb=" N SER A 261 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE A 258 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'A' and resid 117 through 119 removed outlier: 6.537A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE A 258 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.589A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'A' and resid 164 through 169 removed outlier: 3.616A pdb=" N ALA A 247 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'A' and resid 282 through 284 removed outlier: 3.823A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE A 289 " --> pdb=" O CYS A 282 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.761A pdb=" N VAL C 18 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.274A pdb=" N GLU C 10 " --> pdb=" O THR C 114 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N MET C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TRP C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C 40 " --> pdb=" O GLY C 44 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.733A pdb=" N ASP D 74 " --> pdb=" O SER D 71 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.869A pdb=" N GLU D 109 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=21, first strand: chain 'D' and resid 57 through 58 removed outlier: 3.569A pdb=" N ASN D 57 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU D 50 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLN D 41 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE D 52 " --> pdb=" O TRP D 39 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR D 101 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'E' and resid 19 through 20 Processing sheet with id=23, first strand: chain 'E' and resid 33 through 35 Processing sheet with id=24, first strand: chain 'E' and resid 37 through 38 Processing sheet with id=25, first strand: chain 'E' and resid 54 through 57 removed outlier: 6.839A pdb=" N LEU E 54 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'E' and resid 112 through 114 removed outlier: 6.984A pdb=" N SER E 261 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR E 256 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU E 179 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE E 258 " --> pdb=" O LEU E 177 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU E 175 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'E' and resid 117 through 119 removed outlier: 6.537A pdb=" N TYR E 256 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU E 179 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE E 258 " --> pdb=" O LEU E 177 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU E 175 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'E' and resid 136 through 141 removed outlier: 4.588A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'E' and resid 164 through 169 removed outlier: 3.616A pdb=" N ALA E 247 " --> pdb=" O LEU E 164 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'E' and resid 282 through 284 removed outlier: 3.823A pdb=" N CYS E 282 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE E 289 " --> pdb=" O CYS E 282 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'I' and resid 3 through 6 removed outlier: 3.760A pdb=" N VAL I 18 " --> pdb=" O ILE I 83 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.275A pdb=" N GLU I 10 " --> pdb=" O THR I 114 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TRP I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA I 40 " --> pdb=" O GLY I 44 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.732A pdb=" N ASP J 74 " --> pdb=" O SER J 71 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.870A pdb=" N GLU J 109 " --> pdb=" O LEU J 11 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'J' and resid 30 through 31 Processing sheet with id=36, first strand: chain 'J' and resid 57 through 58 removed outlier: 3.569A pdb=" N ASN J 57 " --> pdb=" O TYR J 53 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LEU J 50 " --> pdb=" O GLN J 41 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLN J 41 " --> pdb=" O LEU J 50 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE J 52 " --> pdb=" O TRP J 39 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR J 101 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'K' and resid 19 through 20 Processing sheet with id=38, first strand: chain 'K' and resid 33 through 35 Processing sheet with id=39, first strand: chain 'K' and resid 37 through 38 Processing sheet with id=40, first strand: chain 'K' and resid 54 through 57 removed outlier: 6.840A pdb=" N LEU K 54 " --> pdb=" O VAL K 84 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'K' and resid 112 through 114 removed outlier: 6.984A pdb=" N SER K 261 " --> pdb=" O SER K 113 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR K 256 " --> pdb=" O LEU K 179 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU K 179 " --> pdb=" O TYR K 256 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE K 258 " --> pdb=" O LEU K 177 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU K 175 " --> pdb=" O LEU K 260 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU K 179 " --> pdb=" O PRO K 254 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'K' and resid 117 through 119 removed outlier: 6.537A pdb=" N TYR K 256 " --> pdb=" O LEU K 179 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU K 179 " --> pdb=" O TYR K 256 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE K 258 " --> pdb=" O LEU K 177 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU K 175 " --> pdb=" O LEU K 260 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'K' and resid 136 through 141 removed outlier: 4.589A pdb=" N CYS K 139 " --> pdb=" O SER K 146 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'K' and resid 164 through 169 removed outlier: 3.616A pdb=" N ALA K 247 " --> pdb=" O LEU K 164 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'K' and resid 282 through 284 removed outlier: 3.824A pdb=" N CYS K 282 " --> pdb=" O ILE K 289 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE K 289 " --> pdb=" O CYS K 282 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1197 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2461 1.32 - 1.45: 4221 1.45 - 1.58: 8075 1.58 - 1.71: 0 1.71 - 1.84: 84 Bond restraints: 14841 Sorted by residual: bond pdb=" CA LYS E 123 " pdb=" C LYS E 123 " ideal model delta sigma weight residual 1.527 1.456 0.071 1.35e-02 5.49e+03 2.74e+01 bond pdb=" CA LYS A 123 " pdb=" C LYS A 123 " ideal model delta sigma weight residual 1.527 1.456 0.071 1.35e-02 5.49e+03 2.73e+01 bond pdb=" CA LYS K 123 " pdb=" C LYS K 123 " ideal model delta sigma weight residual 1.527 1.456 0.071 1.35e-02 5.49e+03 2.73e+01 bond pdb=" CA SER E 125 " pdb=" C SER E 125 " ideal model delta sigma weight residual 1.523 1.462 0.061 1.34e-02 5.57e+03 2.10e+01 bond pdb=" CA SER A 125 " pdb=" C SER A 125 " ideal model delta sigma weight residual 1.523 1.462 0.061 1.34e-02 5.57e+03 2.08e+01 ... (remaining 14836 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 19624 2.67 - 5.35: 452 5.35 - 8.02: 57 8.02 - 10.70: 12 10.70 - 13.37: 6 Bond angle restraints: 20151 Sorted by residual: angle pdb=" N GLU A 90 " pdb=" CA GLU A 90 " pdb=" C GLU A 90 " ideal model delta sigma weight residual 111.36 124.73 -13.37 1.09e+00 8.42e-01 1.50e+02 angle pdb=" N GLU E 90 " pdb=" CA GLU E 90 " pdb=" C GLU E 90 " ideal model delta sigma weight residual 111.36 124.71 -13.35 1.09e+00 8.42e-01 1.50e+02 angle pdb=" N GLU K 90 " pdb=" CA GLU K 90 " pdb=" C GLU K 90 " ideal model delta sigma weight residual 111.36 124.70 -13.34 1.09e+00 8.42e-01 1.50e+02 angle pdb=" N ALA C 76 " pdb=" CA ALA C 76 " pdb=" C ALA C 76 " ideal model delta sigma weight residual 109.96 99.51 10.45 1.58e+00 4.01e-01 4.37e+01 angle pdb=" N ALA I 76 " pdb=" CA ALA I 76 " pdb=" C ALA I 76 " ideal model delta sigma weight residual 109.96 99.54 10.42 1.58e+00 4.01e-01 4.35e+01 ... (remaining 20146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 8176 17.70 - 35.40: 725 35.40 - 53.09: 138 53.09 - 70.79: 21 70.79 - 88.49: 18 Dihedral angle restraints: 9078 sinusoidal: 3846 harmonic: 5232 Sorted by residual: dihedral pdb=" CB CYS K 46 " pdb=" SG CYS K 46 " pdb=" SG CYS K 278 " pdb=" CB CYS K 278 " ideal model delta sinusoidal sigma weight residual -86.00 -23.50 -62.50 1 1.00e+01 1.00e-02 5.17e+01 dihedral pdb=" CB CYS A 46 " pdb=" SG CYS A 46 " pdb=" SG CYS A 278 " pdb=" CB CYS A 278 " ideal model delta sinusoidal sigma weight residual -86.00 -23.51 -62.49 1 1.00e+01 1.00e-02 5.17e+01 dihedral pdb=" CB CYS E 46 " pdb=" SG CYS E 46 " pdb=" SG CYS E 278 " pdb=" CB CYS E 278 " ideal model delta sinusoidal sigma weight residual -86.00 -23.54 -62.46 1 1.00e+01 1.00e-02 5.16e+01 ... (remaining 9075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2078 0.105 - 0.209: 148 0.209 - 0.314: 9 0.314 - 0.419: 3 0.419 - 0.523: 3 Chirality restraints: 2241 Sorted by residual: chirality pdb=" CA GLU E 90 " pdb=" N GLU E 90 " pdb=" C GLU E 90 " pdb=" CB GLU E 90 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.85e+00 chirality pdb=" CA GLU A 90 " pdb=" N GLU A 90 " pdb=" C GLU A 90 " pdb=" CB GLU A 90 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.82e+00 chirality pdb=" CA GLU K 90 " pdb=" N GLU K 90 " pdb=" C GLU K 90 " pdb=" CB GLU K 90 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.78e+00 ... (remaining 2238 not shown) Planarity restraints: 2607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 602 " 0.086 2.00e-02 2.50e+03 7.10e-02 6.31e+01 pdb=" C7 NAG K 602 " -0.024 2.00e-02 2.50e+03 pdb=" C8 NAG K 602 " 0.065 2.00e-02 2.50e+03 pdb=" N2 NAG K 602 " -0.113 2.00e-02 2.50e+03 pdb=" O7 NAG K 602 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 602 " -0.086 2.00e-02 2.50e+03 7.10e-02 6.30e+01 pdb=" C7 NAG E 602 " 0.024 2.00e-02 2.50e+03 pdb=" C8 NAG E 602 " -0.065 2.00e-02 2.50e+03 pdb=" N2 NAG E 602 " 0.113 2.00e-02 2.50e+03 pdb=" O7 NAG E 602 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 602 " 0.086 2.00e-02 2.50e+03 7.10e-02 6.30e+01 pdb=" C7 NAG A 602 " -0.024 2.00e-02 2.50e+03 pdb=" C8 NAG A 602 " 0.065 2.00e-02 2.50e+03 pdb=" N2 NAG A 602 " -0.113 2.00e-02 2.50e+03 pdb=" O7 NAG A 602 " -0.015 2.00e-02 2.50e+03 ... (remaining 2604 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3994 2.81 - 3.33: 11085 3.33 - 3.85: 23583 3.85 - 4.38: 27952 4.38 - 4.90: 49802 Nonbonded interactions: 116416 Sorted by model distance: nonbonded pdb=" OG1 THR E 284 " pdb=" O GLY E 287 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR A 284 " pdb=" O GLY A 287 " model vdw 2.284 3.040 nonbonded pdb=" OG1 THR K 284 " pdb=" O GLY K 287 " model vdw 2.284 3.040 nonbonded pdb=" OG SER J 28 " pdb=" OD1 ASP J 30 " model vdw 2.294 3.040 nonbonded pdb=" OG SER H 28 " pdb=" OD1 ASP H 30 " model vdw 2.294 3.040 ... (remaining 116411 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: 0.03 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'C' selection = chain 'I' } ncs_group { reference = chain 'H' selection = chain 'D' selection = chain 'J' } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'G' 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 individual isotropic 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: 5.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.190 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 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 : 0.007 0.071 14877 Z= 0.369 Angle : 1.025 13.371 20241 Z= 0.583 Chirality : 0.059 0.523 2241 Planarity : 0.008 0.071 2592 Dihedral : 14.130 88.488 5670 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.03 % Favored : 94.80 % Rotamer: Outliers : 0.76 % Allowed : 3.63 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % 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: -3.95 (0.16), residues: 1788 helix: -4.60 (0.12), residues: 213 sheet: -1.95 (0.20), residues: 549 loop : -2.62 (0.15), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 220 TYR 0.016 0.002 TYR H 36 PHE 0.022 0.002 PHE E 115 TRP 0.014 0.002 TRP A 64 HIS 0.009 0.001 HIS J 80 Details of bonding type rmsd covalent geometry : bond 0.00697 (14841) covalent geometry : angle 0.99472 (20151) SS BOND : bond 0.00500 ( 18) SS BOND : angle 1.28286 ( 36) hydrogen bonds : bond 0.28351 ( 438) hydrogen bonds : angle 10.90462 ( 1197) link_BETA1-4 : bond 0.00626 ( 3) link_BETA1-4 : angle 1.90445 ( 9) link_NAG-ASN : bond 0.00958 ( 15) link_NAG-ASN : angle 5.26336 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 270 time to evaluate : 0.550 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 38 GLU cc_start: 0.7955 (tp30) cc_final: 0.7631 (tp30) REVERT: A 44 LYS cc_start: 0.6915 (mtmt) cc_final: 0.6602 (mttm) REVERT: A 55 GLN cc_start: 0.8549 (tt0) cc_final: 0.8339 (mt0) REVERT: A 88 ASN cc_start: 0.7597 (m110) cc_final: 0.7117 (p0) REVERT: A 188 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7619 (tp) REVERT: A 192 ARG cc_start: 0.7131 (mtt180) cc_final: 0.6925 (mtt180) REVERT: A 219 LYS cc_start: 0.8285 (tttm) cc_final: 0.7758 (ttmt) REVERT: A 316 ARG cc_start: 0.7963 (mtp85) cc_final: 0.7697 (mtt90) REVERT: A 317 MET cc_start: 0.8330 (mtp) cc_final: 0.7919 (mtp) REVERT: A 383 ASN cc_start: 0.7029 (t0) cc_final: 0.6627 (t0) REVERT: A 407 MET cc_start: 0.6683 (ttp) cc_final: 0.6453 (ttp) REVERT: C 13 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7168 (mmtm) REVERT: E 38 GLU cc_start: 0.7918 (tp30) cc_final: 0.7712 (tp30) REVERT: E 88 ASN cc_start: 0.7637 (m110) cc_final: 0.7099 (p0) REVERT: E 188 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7545 (tp) REVERT: E 219 LYS cc_start: 0.8255 (tttm) cc_final: 0.7718 (ttmt) REVERT: E 281 LYS cc_start: 0.7073 (mmtt) cc_final: 0.6865 (mmtt) REVERT: E 316 ARG cc_start: 0.7881 (mtp85) cc_final: 0.7429 (mtt90) REVERT: E 398 LYS cc_start: 0.8281 (mttm) cc_final: 0.7900 (mttp) REVERT: E 407 MET cc_start: 0.6750 (ttp) cc_final: 0.6398 (ttp) REVERT: I 54 TYR cc_start: 0.7431 (t80) cc_final: 0.7186 (t80) REVERT: K 38 GLU cc_start: 0.8036 (tp30) cc_final: 0.7692 (tp30) REVERT: K 44 LYS cc_start: 0.6884 (mtmt) cc_final: 0.6409 (mtmt) REVERT: K 55 GLN cc_start: 0.8570 (tt0) cc_final: 0.8355 (mt0) REVERT: K 72 GLU cc_start: 0.7669 (tt0) cc_final: 0.7432 (mt-10) REVERT: K 88 ASN cc_start: 0.7613 (m110) cc_final: 0.7169 (p0) REVERT: K 188 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7557 (tp) REVERT: K 192 ARG cc_start: 0.7078 (mtt180) cc_final: 0.6868 (mtt180) REVERT: K 219 LYS cc_start: 0.8330 (tttm) cc_final: 0.7775 (ttmt) REVERT: K 275 MET cc_start: 0.8076 (tpt) cc_final: 0.7513 (tpt) REVERT: K 276 ASN cc_start: 0.7168 (t0) cc_final: 0.6841 (t0) REVERT: K 316 ARG cc_start: 0.7929 (mtp85) cc_final: 0.7682 (mtt90) REVERT: K 317 MET cc_start: 0.8443 (mtp) cc_final: 0.8012 (mtp) REVERT: K 383 ASN cc_start: 0.7032 (t0) cc_final: 0.6642 (t0) outliers start: 12 outliers final: 1 residues processed: 280 average time/residue: 0.1205 time to fit residues: 49.5539 Evaluate side-chains 213 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 208 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain K residue 188 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 GLN F 82 GLN F 84 ASN F 109 GLN H 35 ASN H 41 GLN H 78 ASN A 130 HIS A 184 HIS A 191 GLN A 196 HIS A 199 ASN A 226 GLN A 231 ASN A 250 ASN A 286 GLN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN C 39 GLN C 82 GLN C 84 ASN C 109 GLN D 41 GLN D 78 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 ASN E 130 HIS E 142 ASN E 184 HIS E 191 GLN E 199 ASN E 231 ASN E 250 ASN ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 ASN I 39 GLN I 82 GLN I 84 ASN I 109 GLN J 35 ASN J 41 GLN K 88 ASN K 130 HIS K 142 ASN K 184 HIS K 191 GLN K 231 ASN K 250 ASN K 409 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.141337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.109127 restraints weight = 17662.879| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.25 r_work: 0.2987 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 14877 Z= 0.206 Angle : 0.675 9.110 20241 Z= 0.346 Chirality : 0.044 0.145 2241 Planarity : 0.005 0.047 2592 Dihedral : 5.937 50.974 2333 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.78 % Allowed : 6.93 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % 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: -3.02 (0.17), residues: 1788 helix: -2.34 (0.27), residues: 222 sheet: -1.53 (0.19), residues: 618 loop : -2.23 (0.17), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 220 TYR 0.013 0.001 TYR K 168 PHE 0.017 0.002 PHE K 440 TRP 0.010 0.001 TRP A 64 HIS 0.003 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00493 (14841) covalent geometry : angle 0.66476 (20151) SS BOND : bond 0.00551 ( 18) SS BOND : angle 1.47291 ( 36) hydrogen bonds : bond 0.04340 ( 438) hydrogen bonds : angle 6.63679 ( 1197) link_BETA1-4 : bond 0.00098 ( 3) link_BETA1-4 : angle 1.73949 ( 9) link_NAG-ASN : bond 0.00320 ( 15) link_NAG-ASN : angle 2.17357 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 236 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 2 ILE cc_start: 0.8649 (mm) cc_final: 0.8447 (mm) REVERT: A 44 LYS cc_start: 0.7945 (mtmt) cc_final: 0.7679 (mtpt) REVERT: A 90 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8000 (mm-30) REVERT: A 115 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.7842 (m-10) REVERT: A 275 MET cc_start: 0.8419 (tpt) cc_final: 0.8080 (tpt) REVERT: A 317 MET cc_start: 0.8714 (mtp) cc_final: 0.8457 (mtp) REVERT: A 383 ASN cc_start: 0.8041 (t0) cc_final: 0.7643 (t0) REVERT: A 402 LYS cc_start: 0.8386 (mmtm) cc_final: 0.8110 (mtpt) REVERT: A 407 MET cc_start: 0.8524 (ttp) cc_final: 0.8315 (ttp) REVERT: C 87 LYS cc_start: 0.6818 (mttm) cc_final: 0.6512 (mttt) REVERT: E 44 LYS cc_start: 0.8027 (mtmt) cc_final: 0.7654 (mtpt) REVERT: E 90 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7939 (mm-30) REVERT: E 115 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.7810 (m-10) REVERT: E 252 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.9056 (mt) REVERT: E 276 ASN cc_start: 0.8178 (t0) cc_final: 0.7954 (t0) REVERT: E 402 LYS cc_start: 0.8259 (mmpt) cc_final: 0.8012 (mmmt) REVERT: I 54 TYR cc_start: 0.8512 (t80) cc_final: 0.8207 (t80) REVERT: I 80 TYR cc_start: 0.8628 (m-80) cc_final: 0.8177 (m-80) REVERT: I 104 MET cc_start: 0.8873 (mtm) cc_final: 0.8583 (mtt) REVERT: K 44 LYS cc_start: 0.8001 (mtmt) cc_final: 0.7593 (mtmt) REVERT: K 90 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8066 (mm-30) REVERT: K 115 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.7813 (m-10) REVERT: K 252 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.8763 (mt) REVERT: K 275 MET cc_start: 0.8541 (tpt) cc_final: 0.7926 (tpt) REVERT: K 276 ASN cc_start: 0.8078 (t0) cc_final: 0.7663 (t0) REVERT: K 383 ASN cc_start: 0.8102 (t0) cc_final: 0.7688 (t0) REVERT: K 435 GLU cc_start: 0.8142 (tt0) cc_final: 0.7928 (tt0) outliers start: 28 outliers final: 21 residues processed: 252 average time/residue: 0.1329 time to fit residues: 48.4573 Evaluate side-chains 243 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 115 PHE Chi-restraints excluded: chain K residue 142 ASN Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 252 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 130 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN C 109 GLN D 78 ASN E 196 HIS I 109 GLN ** K 297 ASN ** 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 = 0.3640 r_free = 0.3640 target = 0.142181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.110546 restraints weight = 17753.099| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.28 r_work: 0.3022 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14877 Z= 0.148 Angle : 0.599 9.748 20241 Z= 0.305 Chirality : 0.042 0.136 2241 Planarity : 0.004 0.044 2592 Dihedral : 5.288 25.633 2323 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.97 % Allowed : 9.73 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % 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: -2.47 (0.18), residues: 1788 helix: -0.96 (0.33), residues: 222 sheet: -1.32 (0.20), residues: 588 loop : -2.01 (0.17), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 436 TYR 0.011 0.001 TYR C 60 PHE 0.021 0.001 PHE A 440 TRP 0.011 0.001 TRP F 107 HIS 0.003 0.001 HIS K 184 Details of bonding type rmsd covalent geometry : bond 0.00351 (14841) covalent geometry : angle 0.58889 (20151) SS BOND : bond 0.00474 ( 18) SS BOND : angle 0.98962 ( 36) hydrogen bonds : bond 0.03674 ( 438) hydrogen bonds : angle 6.08218 ( 1197) link_BETA1-4 : bond 0.00082 ( 3) link_BETA1-4 : angle 1.55642 ( 9) link_NAG-ASN : bond 0.00301 ( 15) link_NAG-ASN : angle 2.15941 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 227 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 109 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8311 (pp30) REVERT: A 88 ASN cc_start: 0.7731 (m110) cc_final: 0.7355 (p0) REVERT: A 90 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8027 (mm-30) REVERT: A 115 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7752 (m-10) REVERT: A 383 ASN cc_start: 0.8032 (t0) cc_final: 0.7649 (t0) REVERT: A 402 LYS cc_start: 0.8300 (mmtm) cc_final: 0.8058 (mmmt) REVERT: C 109 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.7858 (pp30) REVERT: E 44 LYS cc_start: 0.7883 (mtmt) cc_final: 0.7454 (mtpt) REVERT: E 88 ASN cc_start: 0.7755 (m-40) cc_final: 0.7543 (p0) REVERT: E 90 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7959 (mm-30) REVERT: E 115 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7770 (m-10) REVERT: E 276 ASN cc_start: 0.8232 (t0) cc_final: 0.7987 (t0) REVERT: I 54 TYR cc_start: 0.8325 (t80) cc_final: 0.8027 (t80) REVERT: I 80 TYR cc_start: 0.8610 (m-80) cc_final: 0.8168 (m-80) REVERT: K 88 ASN cc_start: 0.7711 (m-40) cc_final: 0.7289 (p0) REVERT: K 90 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8107 (mm-30) REVERT: K 115 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7745 (m-10) REVERT: K 383 ASN cc_start: 0.8074 (t0) cc_final: 0.7653 (t0) outliers start: 31 outliers final: 19 residues processed: 240 average time/residue: 0.1166 time to fit residues: 41.5904 Evaluate side-chains 235 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 115 PHE Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 187 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 170 optimal weight: 3.9990 chunk 159 optimal weight: 0.5980 chunk 175 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 157 optimal weight: 0.4980 chunk 92 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 148 optimal weight: 0.3980 chunk 126 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN A 199 ASN C 109 GLN D 78 ASN I 109 GLN K 196 HIS ** K 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.147013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.116225 restraints weight = 17646.644| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.12 r_work: 0.3128 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14877 Z= 0.110 Angle : 0.565 9.089 20241 Z= 0.287 Chirality : 0.041 0.137 2241 Planarity : 0.004 0.040 2592 Dihedral : 4.981 28.475 2322 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.91 % Allowed : 12.02 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % 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: -2.04 (0.18), residues: 1788 helix: -0.37 (0.36), residues: 222 sheet: -1.11 (0.20), residues: 597 loop : -1.74 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 436 TYR 0.009 0.001 TYR C 60 PHE 0.023 0.001 PHE A 440 TRP 0.011 0.001 TRP C 107 HIS 0.002 0.001 HIS E 184 Details of bonding type rmsd covalent geometry : bond 0.00259 (14841) covalent geometry : angle 0.55119 (20151) SS BOND : bond 0.00425 ( 18) SS BOND : angle 2.02766 ( 36) hydrogen bonds : bond 0.03119 ( 438) hydrogen bonds : angle 5.72126 ( 1197) link_BETA1-4 : bond 0.00160 ( 3) link_BETA1-4 : angle 1.36505 ( 9) link_NAG-ASN : bond 0.00242 ( 15) link_NAG-ASN : angle 2.02142 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 218 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 109 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8166 (pm20) REVERT: A 90 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7978 (mm-30) REVERT: A 115 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7654 (m-10) REVERT: A 383 ASN cc_start: 0.8102 (t0) cc_final: 0.7727 (t0) REVERT: A 442 ASP cc_start: 0.7999 (t70) cc_final: 0.7588 (t0) REVERT: C 109 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8045 (pm20) REVERT: E 44 LYS cc_start: 0.7816 (mtmt) cc_final: 0.7514 (mtmt) REVERT: E 90 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7949 (mm-30) REVERT: E 115 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7676 (m-10) REVERT: I 54 TYR cc_start: 0.8301 (t80) cc_final: 0.7996 (t80) REVERT: I 80 TYR cc_start: 0.8590 (m-80) cc_final: 0.8138 (m-80) REVERT: I 104 MET cc_start: 0.8722 (mtm) cc_final: 0.8477 (mtt) REVERT: I 109 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8158 (pm20) REVERT: K 88 ASN cc_start: 0.7559 (m-40) cc_final: 0.7289 (p0) REVERT: K 90 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8041 (mm-30) REVERT: K 115 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7652 (m-10) REVERT: K 383 ASN cc_start: 0.8158 (t0) cc_final: 0.7763 (t0) REVERT: K 398 LYS cc_start: 0.8825 (mttm) cc_final: 0.8419 (mtpp) outliers start: 30 outliers final: 20 residues processed: 229 average time/residue: 0.1276 time to fit residues: 42.9594 Evaluate side-chains 239 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 213 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain K residue 115 PHE Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 179 LEU Chi-restraints excluded: chain K residue 187 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 166 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 131 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN D 78 ASN E 142 ASN K 142 ASN K 248 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.142207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.110617 restraints weight = 17701.892| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.29 r_work: 0.3040 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14877 Z= 0.155 Angle : 0.584 10.107 20241 Z= 0.294 Chirality : 0.042 0.136 2241 Planarity : 0.004 0.040 2592 Dihedral : 4.933 26.085 2322 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.61 % Allowed : 12.21 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % 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: -1.85 (0.19), residues: 1788 helix: -0.21 (0.36), residues: 222 sheet: -0.98 (0.20), residues: 597 loop : -1.63 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 436 TYR 0.010 0.001 TYR C 80 PHE 0.027 0.001 PHE A 440 TRP 0.011 0.001 TRP C 107 HIS 0.003 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00375 (14841) covalent geometry : angle 0.57142 (20151) SS BOND : bond 0.00446 ( 18) SS BOND : angle 1.71015 ( 36) hydrogen bonds : bond 0.03173 ( 438) hydrogen bonds : angle 5.62651 ( 1197) link_BETA1-4 : bond 0.00145 ( 3) link_BETA1-4 : angle 1.49562 ( 9) link_NAG-ASN : bond 0.00308 ( 15) link_NAG-ASN : angle 2.03727 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 216 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8115 (mm-30) REVERT: A 115 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7763 (m-10) REVERT: A 383 ASN cc_start: 0.8053 (t0) cc_final: 0.7664 (t0) REVERT: A 442 ASP cc_start: 0.8009 (t70) cc_final: 0.7614 (t0) REVERT: C 109 GLN cc_start: 0.8538 (pp30) cc_final: 0.8296 (pm20) REVERT: E 44 LYS cc_start: 0.7834 (mtmt) cc_final: 0.7474 (mtpt) REVERT: E 90 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8038 (mm-30) REVERT: E 115 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7711 (m-10) REVERT: I 80 TYR cc_start: 0.8643 (m-80) cc_final: 0.8175 (m-80) REVERT: I 109 GLN cc_start: 0.8601 (pp30) cc_final: 0.8377 (pm20) REVERT: K 88 ASN cc_start: 0.7772 (m-40) cc_final: 0.7358 (p0) REVERT: K 90 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8138 (mm-30) REVERT: K 115 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7744 (m-10) REVERT: K 383 ASN cc_start: 0.8098 (t0) cc_final: 0.7673 (t0) REVERT: K 398 LYS cc_start: 0.8792 (mttm) cc_final: 0.8376 (mtpp) REVERT: K 429 LEU cc_start: 0.8901 (tt) cc_final: 0.8691 (tp) outliers start: 41 outliers final: 29 residues processed: 238 average time/residue: 0.1198 time to fit residues: 42.2853 Evaluate side-chains 242 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 115 PHE Chi-restraints excluded: chain K residue 142 ASN Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 179 LEU Chi-restraints excluded: chain K residue 187 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 0.0570 chunk 14 optimal weight: 2.9990 chunk 147 optimal weight: 0.5980 chunk 141 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.2702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN E 142 ASN K 142 ASN K 248 ASN K 297 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.140992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.109439 restraints weight = 17718.104| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.27 r_work: 0.2991 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14877 Z= 0.187 Angle : 0.605 11.104 20241 Z= 0.304 Chirality : 0.042 0.136 2241 Planarity : 0.004 0.044 2592 Dihedral : 4.964 24.884 2322 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.80 % Allowed : 12.66 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % 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: -1.77 (0.19), residues: 1788 helix: -0.11 (0.36), residues: 222 sheet: -0.91 (0.20), residues: 597 loop : -1.59 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 436 TYR 0.010 0.001 TYR C 60 PHE 0.028 0.002 PHE A 440 TRP 0.008 0.001 TRP A 64 HIS 0.004 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00453 (14841) covalent geometry : angle 0.59414 (20151) SS BOND : bond 0.00502 ( 18) SS BOND : angle 1.46469 ( 36) hydrogen bonds : bond 0.03268 ( 438) hydrogen bonds : angle 5.59103 ( 1197) link_BETA1-4 : bond 0.00134 ( 3) link_BETA1-4 : angle 1.58321 ( 9) link_NAG-ASN : bond 0.00350 ( 15) link_NAG-ASN : angle 2.05153 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 218 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8153 (mm-30) REVERT: A 115 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7800 (m-10) REVERT: A 292 SER cc_start: 0.9203 (t) cc_final: 0.8892 (p) REVERT: A 383 ASN cc_start: 0.8069 (t0) cc_final: 0.7689 (t0) REVERT: C 109 GLN cc_start: 0.8556 (pp30) cc_final: 0.8252 (pm20) REVERT: E 44 LYS cc_start: 0.7840 (mtmt) cc_final: 0.7397 (mtpt) REVERT: E 90 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8102 (mm-30) REVERT: E 115 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.7775 (m-10) REVERT: E 442 ASP cc_start: 0.7878 (t70) cc_final: 0.7535 (t0) REVERT: I 80 TYR cc_start: 0.8656 (m-80) cc_final: 0.8180 (m-80) REVERT: I 109 GLN cc_start: 0.8641 (pp30) cc_final: 0.8362 (pm20) REVERT: K 88 ASN cc_start: 0.7749 (m-40) cc_final: 0.7331 (p0) REVERT: K 90 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8144 (mm-30) REVERT: K 115 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7753 (m-10) REVERT: K 252 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8766 (mt) REVERT: K 279 ASP cc_start: 0.7342 (OUTLIER) cc_final: 0.7019 (t0) REVERT: K 383 ASN cc_start: 0.8118 (t0) cc_final: 0.7702 (t0) REVERT: K 429 LEU cc_start: 0.8915 (tt) cc_final: 0.8696 (tp) outliers start: 44 outliers final: 33 residues processed: 241 average time/residue: 0.1158 time to fit residues: 41.5945 Evaluate side-chains 255 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 217 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 115 PHE Chi-restraints excluded: chain K residue 142 ASN Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 179 LEU Chi-restraints excluded: chain K residue 187 ASN Chi-restraints excluded: chain K residue 252 ILE Chi-restraints excluded: chain K residue 279 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 90 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 10 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 148 optimal weight: 0.0170 overall best weight: 1.1024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN K 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.140263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.107790 restraints weight = 17637.975| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.28 r_work: 0.2964 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14877 Z= 0.167 Angle : 0.598 12.361 20241 Z= 0.300 Chirality : 0.042 0.136 2241 Planarity : 0.004 0.044 2592 Dihedral : 4.911 24.834 2322 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.42 % Allowed : 14.44 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % 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: -1.60 (0.19), residues: 1788 helix: 0.02 (0.36), residues: 222 sheet: -0.79 (0.20), residues: 630 loop : -1.50 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 436 TYR 0.010 0.001 TYR F 80 PHE 0.028 0.001 PHE A 440 TRP 0.008 0.001 TRP E 64 HIS 0.003 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00405 (14841) covalent geometry : angle 0.58537 (20151) SS BOND : bond 0.00472 ( 18) SS BOND : angle 1.85978 ( 36) hydrogen bonds : bond 0.03169 ( 438) hydrogen bonds : angle 5.53936 ( 1197) link_BETA1-4 : bond 0.00099 ( 3) link_BETA1-4 : angle 1.51541 ( 9) link_NAG-ASN : bond 0.00332 ( 15) link_NAG-ASN : angle 2.03194 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 205 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8231 (mm-30) REVERT: A 115 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7828 (m-10) REVERT: A 292 SER cc_start: 0.9211 (t) cc_final: 0.8906 (p) REVERT: A 383 ASN cc_start: 0.8087 (t0) cc_final: 0.7717 (t0) REVERT: E 90 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8168 (mm-30) REVERT: E 115 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7846 (m-10) REVERT: E 442 ASP cc_start: 0.7852 (t70) cc_final: 0.7505 (t0) REVERT: I 80 TYR cc_start: 0.8705 (m-80) cc_final: 0.8233 (m-80) REVERT: I 109 GLN cc_start: 0.8621 (pp30) cc_final: 0.8195 (pm20) REVERT: K 88 ASN cc_start: 0.7827 (m-40) cc_final: 0.7375 (p0) REVERT: K 90 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8190 (mm-30) REVERT: K 115 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.7848 (m-10) REVERT: K 279 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.7120 (t0) REVERT: K 383 ASN cc_start: 0.8119 (t0) cc_final: 0.7705 (t0) REVERT: K 429 LEU cc_start: 0.8963 (tt) cc_final: 0.8747 (tp) outliers start: 38 outliers final: 32 residues processed: 222 average time/residue: 0.1102 time to fit residues: 36.2015 Evaluate side-chains 241 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 205 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 115 PHE Chi-restraints excluded: chain K residue 142 ASN Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 179 LEU Chi-restraints excluded: chain K residue 187 ASN Chi-restraints excluded: chain K residue 279 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 58 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 53 optimal weight: 0.0770 chunk 62 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN C 109 GLN E 142 ASN I 109 GLN J 6 GLN K 142 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.140537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.108743 restraints weight = 17690.908| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.24 r_work: 0.2980 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14877 Z= 0.148 Angle : 0.580 12.247 20241 Z= 0.291 Chirality : 0.042 0.136 2241 Planarity : 0.004 0.043 2592 Dihedral : 4.821 24.665 2322 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.86 % Allowed : 14.31 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % 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: -1.47 (0.19), residues: 1788 helix: 0.15 (0.36), residues: 222 sheet: -0.72 (0.20), residues: 630 loop : -1.40 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 436 TYR 0.010 0.001 TYR C 60 PHE 0.029 0.001 PHE A 440 TRP 0.008 0.001 TRP E 64 HIS 0.003 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00357 (14841) covalent geometry : angle 0.56816 (20151) SS BOND : bond 0.00436 ( 18) SS BOND : angle 1.65761 ( 36) hydrogen bonds : bond 0.03058 ( 438) hydrogen bonds : angle 5.47393 ( 1197) link_BETA1-4 : bond 0.00114 ( 3) link_BETA1-4 : angle 1.44752 ( 9) link_NAG-ASN : bond 0.00315 ( 15) link_NAG-ASN : angle 2.00152 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 210 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8223 (mm-30) REVERT: A 115 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7848 (m-10) REVERT: A 292 SER cc_start: 0.9197 (t) cc_final: 0.8904 (p) REVERT: A 383 ASN cc_start: 0.8074 (t0) cc_final: 0.7702 (t0) REVERT: E 90 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8195 (mm-30) REVERT: E 115 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7802 (m-10) REVERT: E 292 SER cc_start: 0.9116 (t) cc_final: 0.8894 (p) REVERT: E 442 ASP cc_start: 0.7841 (t70) cc_final: 0.7510 (t0) REVERT: I 80 TYR cc_start: 0.8693 (m-80) cc_final: 0.8232 (m-80) REVERT: I 109 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8207 (pm20) REVERT: K 88 ASN cc_start: 0.7834 (m-40) cc_final: 0.7442 (p0) REVERT: K 90 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8197 (mm-30) REVERT: K 115 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.7802 (m-10) REVERT: K 279 ASP cc_start: 0.7396 (OUTLIER) cc_final: 0.7088 (t0) REVERT: K 383 ASN cc_start: 0.8112 (t0) cc_final: 0.7699 (t0) REVERT: K 429 LEU cc_start: 0.8957 (tt) cc_final: 0.8741 (tp) outliers start: 45 outliers final: 36 residues processed: 230 average time/residue: 0.1174 time to fit residues: 39.9477 Evaluate side-chains 247 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 206 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 115 PHE Chi-restraints excluded: chain K residue 142 ASN Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 179 LEU Chi-restraints excluded: chain K residue 187 ASN Chi-restraints excluded: chain K residue 279 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN A 199 ASN ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN E 142 ASN E 248 ASN I 6 GLN ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.140598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.109142 restraints weight = 17794.587| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.22 r_work: 0.2934 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14877 Z= 0.167 Angle : 0.595 12.831 20241 Z= 0.299 Chirality : 0.042 0.172 2241 Planarity : 0.004 0.043 2592 Dihedral : 4.829 24.568 2322 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.54 % Allowed : 14.69 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.19), residues: 1788 helix: 0.21 (0.36), residues: 222 sheet: -0.68 (0.20), residues: 636 loop : -1.47 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 436 TYR 0.012 0.001 TYR C 27 PHE 0.030 0.001 PHE A 440 TRP 0.008 0.001 TRP E 64 HIS 0.008 0.001 HIS E 141 Details of bonding type rmsd covalent geometry : bond 0.00404 (14841) covalent geometry : angle 0.58382 (20151) SS BOND : bond 0.00452 ( 18) SS BOND : angle 1.64881 ( 36) hydrogen bonds : bond 0.03126 ( 438) hydrogen bonds : angle 5.47092 ( 1197) link_BETA1-4 : bond 0.00201 ( 3) link_BETA1-4 : angle 1.49008 ( 9) link_NAG-ASN : bond 0.00331 ( 15) link_NAG-ASN : angle 1.99548 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8254 (mm-30) REVERT: A 115 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7826 (m-10) REVERT: A 292 SER cc_start: 0.9204 (t) cc_final: 0.8914 (p) REVERT: A 383 ASN cc_start: 0.8096 (t0) cc_final: 0.7719 (t0) REVERT: E 90 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8221 (mm-30) REVERT: E 115 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7795 (m-10) REVERT: E 292 SER cc_start: 0.9135 (t) cc_final: 0.8917 (p) REVERT: E 442 ASP cc_start: 0.7856 (t70) cc_final: 0.7525 (t0) REVERT: I 80 TYR cc_start: 0.8711 (m-80) cc_final: 0.8249 (m-80) REVERT: K 88 ASN cc_start: 0.7898 (m-40) cc_final: 0.7559 (p0) REVERT: K 90 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8212 (mm-30) REVERT: K 115 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7835 (m-10) REVERT: K 252 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.8798 (mt) REVERT: K 279 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.7209 (t0) REVERT: K 383 ASN cc_start: 0.8140 (t0) cc_final: 0.7730 (t0) outliers start: 40 outliers final: 33 residues processed: 220 average time/residue: 0.1055 time to fit residues: 34.4038 Evaluate side-chains 238 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 200 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 115 PHE Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 179 LEU Chi-restraints excluded: chain K residue 187 ASN Chi-restraints excluded: chain K residue 252 ILE Chi-restraints excluded: chain K residue 279 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 46 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 137 optimal weight: 0.1980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 ASN I 6 GLN ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 ASN K 199 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.141861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.110563 restraints weight = 17666.346| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.40 r_work: 0.3085 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14877 Z= 0.180 Angle : 0.605 13.318 20241 Z= 0.304 Chirality : 0.042 0.155 2241 Planarity : 0.004 0.044 2592 Dihedral : 4.847 24.887 2322 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.74 % Allowed : 14.38 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % 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: -1.45 (0.19), residues: 1788 helix: 0.24 (0.36), residues: 222 sheet: -0.65 (0.20), residues: 636 loop : -1.47 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 436 TYR 0.011 0.001 TYR C 60 PHE 0.031 0.002 PHE A 440 TRP 0.009 0.001 TRP A 64 HIS 0.007 0.001 HIS E 141 Details of bonding type rmsd covalent geometry : bond 0.00437 (14841) covalent geometry : angle 0.59381 (20151) SS BOND : bond 0.00489 ( 18) SS BOND : angle 1.62084 ( 36) hydrogen bonds : bond 0.03165 ( 438) hydrogen bonds : angle 5.50928 ( 1197) link_BETA1-4 : bond 0.00115 ( 3) link_BETA1-4 : angle 1.51954 ( 9) link_NAG-ASN : bond 0.00349 ( 15) link_NAG-ASN : angle 2.00247 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 207 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8186 (mm-30) REVERT: A 115 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7762 (m-10) REVERT: A 292 SER cc_start: 0.9195 (t) cc_final: 0.8904 (p) REVERT: A 383 ASN cc_start: 0.8116 (t0) cc_final: 0.7747 (t0) REVERT: E 90 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8137 (mm-30) REVERT: E 115 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7724 (m-10) REVERT: E 292 SER cc_start: 0.9120 (t) cc_final: 0.8900 (p) REVERT: E 442 ASP cc_start: 0.7819 (t70) cc_final: 0.7501 (t0) REVERT: I 80 TYR cc_start: 0.8698 (m-80) cc_final: 0.8160 (m-80) REVERT: K 88 ASN cc_start: 0.7813 (m-40) cc_final: 0.7604 (p0) REVERT: K 90 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8163 (mm-30) REVERT: K 115 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7730 (m-10) REVERT: K 252 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.8787 (mt) REVERT: K 279 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7210 (t0) REVERT: K 383 ASN cc_start: 0.8155 (t0) cc_final: 0.7749 (t0) outliers start: 43 outliers final: 38 residues processed: 224 average time/residue: 0.1272 time to fit residues: 41.9224 Evaluate side-chains 249 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 206 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 115 PHE Chi-restraints excluded: chain K residue 142 ASN Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 179 LEU Chi-restraints excluded: chain K residue 187 ASN Chi-restraints excluded: chain K residue 199 ASN Chi-restraints excluded: chain K residue 252 ILE Chi-restraints excluded: chain K residue 279 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 158 optimal weight: 0.0870 chunk 136 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 86 optimal weight: 0.0970 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 112 optimal weight: 0.2980 chunk 176 optimal weight: 3.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.142205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.110776 restraints weight = 17683.430| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.41 r_work: 0.3047 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.130 14877 Z= 0.214 Angle : 1.036 59.054 20241 Z= 0.619 Chirality : 0.047 0.758 2241 Planarity : 0.005 0.127 2592 Dihedral : 4.921 39.631 2322 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.67 % Allowed : 14.57 % Favored : 82.76 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.46 (0.19), residues: 1788 helix: 0.26 (0.36), residues: 222 sheet: -0.65 (0.20), residues: 636 loop : -1.49 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 436 TYR 0.010 0.001 TYR C 60 PHE 0.029 0.001 PHE A 440 TRP 0.008 0.001 TRP A 64 HIS 0.004 0.001 HIS E 141 Details of bonding type rmsd covalent geometry : bond 0.00451 (14841) covalent geometry : angle 1.03083 (20151) SS BOND : bond 0.00406 ( 18) SS BOND : angle 1.77017 ( 36) hydrogen bonds : bond 0.03103 ( 438) hydrogen bonds : angle 5.50947 ( 1197) link_BETA1-4 : bond 0.01078 ( 3) link_BETA1-4 : angle 1.59893 ( 9) link_NAG-ASN : bond 0.00337 ( 15) link_NAG-ASN : angle 2.01281 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4131.03 seconds wall clock time: 71 minutes 19.79 seconds (4279.79 seconds total)