Starting phenix.real_space_refine on Fri Jun 13 03:16:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yhk_33831/06_2025/7yhk_33831.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yhk_33831/06_2025/7yhk_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_33831/06_2025/7yhk_33831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yhk_33831/06_2025/7yhk_33831.map" model { file = "/net/cci-nas-00/data/ceres_data/7yhk_33831/06_2025/7yhk_33831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yhk_33831/06_2025/7yhk_33831.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14502 Number of models: 1 Model: "" Number of chains: 5 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 Chain: "C" 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: "D" 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} Restraints were copied for chains: F, I, G, L, E, K, H, J Time building chain proxies: 9.06, per 1000 atoms: 0.62 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=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 4.12 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 2.16 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: 4.98 Time building geometry restraints manager: 4.79 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: 8152 17.70 - 35.40: 707 35.40 - 53.09: 129 53.09 - 70.79: 18 70.79 - 88.49: 18 Dihedral angle restraints: 9024 sinusoidal: 3792 harmonic: 5232 Sorted by residual: dihedral pdb=" CA CYS E 278 " pdb=" C CYS E 278 " pdb=" N ASP E 279 " pdb=" CA ASP E 279 " ideal model delta harmonic sigma weight residual 180.00 150.37 29.63 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA CYS K 278 " pdb=" C CYS K 278 " pdb=" N ASP K 279 " pdb=" CA ASP K 279 " ideal model delta harmonic sigma weight residual 180.00 150.39 29.61 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA CYS A 278 " pdb=" C CYS A 278 " pdb=" N ASP A 279 " pdb=" CA ASP A 279 " ideal model delta harmonic sigma weight residual 180.00 150.40 29.60 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 9021 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: 2.02 - 2.60: 144 2.60 - 3.17: 10754 3.17 - 3.75: 20994 3.75 - 4.32: 31320 4.32 - 4.90: 53258 Nonbonded interactions: 116470 Sorted by model distance: nonbonded pdb=" SG CYS A 282 " pdb=" SG CYS A 306 " model vdw 2.022 3.760 nonbonded pdb=" SG CYS E 282 " pdb=" SG CYS E 306 " model vdw 2.022 3.760 nonbonded pdb=" SG CYS K 282 " pdb=" SG CYS K 306 " model vdw 2.022 3.760 nonbonded pdb=" SG CYS K 59 " pdb=" SG CYS K 71 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS E 59 " pdb=" SG CYS E 71 " model vdw 2.026 3.760 ... (remaining 116465 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: 0.12 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } 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: 6.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 37.490 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.910 ------------------------------------------------------------------------------- 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 14859 Z= 0.369 Angle : 1.025 13.371 20205 Z= 0.583 Chirality : 0.059 0.523 2241 Planarity : 0.008 0.071 2592 Dihedral : 14.130 88.488 5670 Min Nonbonded Distance : 2.022 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.014 0.002 TRP A 64 HIS 0.009 0.001 HIS J 80 PHE 0.022 0.002 PHE E 115 TYR 0.016 0.002 TYR H 36 ARG 0.011 0.001 ARG K 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00958 ( 15) link_NAG-ASN : angle 5.26336 ( 45) link_BETA1-4 : bond 0.00626 ( 3) link_BETA1-4 : angle 1.90445 ( 9) hydrogen bonds : bond 0.28351 ( 438) hydrogen bonds : angle 10.90462 ( 1197) covalent geometry : bond 0.00697 (14841) covalent geometry : angle 0.99472 (20151) *********************** 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 : 1.601 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: 0.2765 time to fit residues: 112.6170 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 : 1.717 ------------------------------------------------------------------------------- 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 149 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 71 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 88 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 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 409 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.144181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.111974 restraints weight = 17427.009| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.24 r_work: 0.3101 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14859 Z= 0.143 Angle : 0.620 8.441 20205 Z= 0.321 Chirality : 0.042 0.140 2241 Planarity : 0.005 0.044 2592 Dihedral : 5.799 51.702 2333 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.34 % Allowed : 7.89 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.17), residues: 1788 helix: -2.23 (0.27), residues: 222 sheet: -1.59 (0.19), residues: 588 loop : -2.16 (0.17), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 422 HIS 0.002 0.001 HIS E 130 PHE 0.016 0.001 PHE K 440 TYR 0.010 0.001 TYR C 60 ARG 0.004 0.000 ARG A 436 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 15) link_NAG-ASN : angle 2.07220 ( 45) link_BETA1-4 : bond 0.00284 ( 3) link_BETA1-4 : angle 1.54620 ( 9) hydrogen bonds : bond 0.04040 ( 438) hydrogen bonds : angle 6.67940 ( 1197) covalent geometry : bond 0.00335 (14841) covalent geometry : angle 0.61218 (20151) *********************** 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: 21 poor density : 243 time to evaluate : 2.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 87 LYS cc_start: 0.6789 (mttm) cc_final: 0.6471 (mttt) REVERT: A 88 ASN cc_start: 0.7787 (m-40) cc_final: 0.7364 (p0) REVERT: A 90 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7932 (mm-30) REVERT: A 275 MET cc_start: 0.8419 (tpt) cc_final: 0.8117 (tpt) REVERT: A 317 MET cc_start: 0.8593 (mtp) cc_final: 0.8346 (tpp) REVERT: A 383 ASN cc_start: 0.8054 (t0) cc_final: 0.7647 (t0) REVERT: A 402 LYS cc_start: 0.8359 (mmtm) cc_final: 0.8092 (mmmt) REVERT: A 407 MET cc_start: 0.8485 (ttp) cc_final: 0.8284 (ttp) REVERT: E 44 LYS cc_start: 0.7995 (mtmt) cc_final: 0.7679 (mtpt) REVERT: E 88 ASN cc_start: 0.7743 (m-40) cc_final: 0.7271 (p0) REVERT: E 90 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7901 (mm-30) REVERT: E 276 ASN cc_start: 0.8149 (t0) cc_final: 0.7845 (t0) REVERT: E 402 LYS cc_start: 0.8288 (mmpt) cc_final: 0.8088 (mtpt) REVERT: I 54 TYR cc_start: 0.8464 (t80) cc_final: 0.8170 (t80) REVERT: I 82 GLN cc_start: 0.8000 (tt0) cc_final: 0.7744 (tt0) REVERT: K 88 ASN cc_start: 0.7671 (m-40) cc_final: 0.7338 (p0) REVERT: K 90 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7958 (mm-30) REVERT: K 275 MET cc_start: 0.8522 (tpt) cc_final: 0.8037 (tpt) REVERT: K 276 ASN cc_start: 0.7966 (t0) cc_final: 0.7640 (t0) REVERT: K 383 ASN cc_start: 0.8092 (t0) cc_final: 0.7677 (t0) outliers start: 21 outliers final: 20 residues processed: 252 average time/residue: 0.2979 time to fit residues: 108.8405 Evaluate side-chains 238 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 218 time to evaluate : 1.927 ------------------------------------------------------------------------------- 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 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 142 ASN Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 199 ASN 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 81 SER Chi-restraints excluded: chain K residue 142 ASN Chi-restraints excluded: chain K residue 160 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 171 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 6 GLN F 109 GLN A 226 GLN A 411 ASN C 109 GLN D 78 ASN E 196 HIS I 6 GLN I 109 GLN K 196 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.138012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.106799 restraints weight = 17670.584| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.20 r_work: 0.2923 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 14859 Z= 0.281 Angle : 0.696 11.603 20205 Z= 0.352 Chirality : 0.045 0.143 2241 Planarity : 0.005 0.049 2592 Dihedral : 5.621 26.258 2323 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.61 % Allowed : 9.73 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.18), residues: 1788 helix: -1.14 (0.32), residues: 222 sheet: -1.37 (0.19), residues: 624 loop : -2.04 (0.18), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 107 HIS 0.005 0.001 HIS A 184 PHE 0.015 0.002 PHE F 106 TYR 0.013 0.002 TYR J 36 ARG 0.006 0.001 ARG K 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 15) link_NAG-ASN : angle 2.25539 ( 45) link_BETA1-4 : bond 0.00315 ( 3) link_BETA1-4 : angle 2.07176 ( 9) hydrogen bonds : bond 0.04227 ( 438) hydrogen bonds : angle 6.27710 ( 1197) covalent geometry : bond 0.00681 (14841) covalent geometry : angle 0.68689 (20151) *********************** 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 260 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 219 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 23 CYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8656 (t) REVERT: A 90 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8132 (mm-30) REVERT: A 115 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.7965 (m-10) REVERT: A 317 MET cc_start: 0.8760 (mtp) cc_final: 0.8352 (mtp) REVERT: A 383 ASN cc_start: 0.8091 (t0) cc_final: 0.7705 (t0) REVERT: A 402 LYS cc_start: 0.8352 (mmtm) cc_final: 0.8099 (mmmt) REVERT: C 87 LYS cc_start: 0.6794 (mttm) cc_final: 0.6476 (mttt) REVERT: C 104 MET cc_start: 0.9009 (mtm) cc_final: 0.8761 (mtm) REVERT: E 44 LYS cc_start: 0.7971 (mtmt) cc_final: 0.7602 (mtpt) REVERT: E 90 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8132 (mm-30) REVERT: E 115 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.7950 (m-10) REVERT: E 276 ASN cc_start: 0.8323 (t0) cc_final: 0.8047 (t0) REVERT: E 402 LYS cc_start: 0.8276 (mmpt) cc_final: 0.8033 (mtpt) REVERT: I 54 TYR cc_start: 0.8456 (t80) cc_final: 0.8164 (t80) REVERT: I 80 TYR cc_start: 0.8667 (m-80) cc_final: 0.8139 (m-80) REVERT: I 104 MET cc_start: 0.8963 (mtm) cc_final: 0.8758 (mtt) REVERT: K 90 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8198 (mm-30) REVERT: K 115 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.7914 (m-10) REVERT: K 252 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.8852 (mt) REVERT: K 383 ASN cc_start: 0.8156 (t0) cc_final: 0.7731 (t0) outliers start: 41 outliers final: 28 residues processed: 238 average time/residue: 0.2593 time to fit residues: 91.8165 Evaluate side-chains 242 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 209 time to evaluate : 1.783 ------------------------------------------------------------------------------- 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 H residue 23 CYS 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 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 D residue 79 ILE 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 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 79 ILE 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 160 LEU Chi-restraints excluded: chain K residue 179 LEU Chi-restraints excluded: chain K residue 187 ASN Chi-restraints excluded: chain K residue 203 SER Chi-restraints excluded: chain K residue 252 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 118 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 140 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 173 optimal weight: 0.1980 chunk 59 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN H 6 GLN A 411 ASN C 109 GLN E 55 GLN E 142 ASN E 297 ASN I 109 GLN K 142 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.139769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.107836 restraints weight = 17655.432| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.31 r_work: 0.2910 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14859 Z= 0.164 Angle : 0.597 11.913 20205 Z= 0.301 Chirality : 0.042 0.134 2241 Planarity : 0.004 0.044 2592 Dihedral : 5.249 25.532 2322 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.80 % Allowed : 11.90 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.18), residues: 1788 helix: -0.61 (0.35), residues: 222 sheet: -1.19 (0.20), residues: 627 loop : -1.80 (0.18), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 107 HIS 0.003 0.001 HIS K 184 PHE 0.020 0.001 PHE K 440 TYR 0.010 0.001 TYR C 60 ARG 0.004 0.000 ARG E 436 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 15) link_NAG-ASN : angle 2.06710 ( 45) link_BETA1-4 : bond 0.00135 ( 3) link_BETA1-4 : angle 1.61922 ( 9) hydrogen bonds : bond 0.03347 ( 438) hydrogen bonds : angle 5.88489 ( 1197) covalent geometry : bond 0.00394 (14841) covalent geometry : angle 0.58890 (20151) *********************** 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 256 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 212 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 109 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8128 (pm20) REVERT: A 88 ASN cc_start: 0.7847 (m-40) cc_final: 0.7419 (p0) REVERT: A 90 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8115 (mm-30) REVERT: A 115 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.7844 (m-10) REVERT: A 317 MET cc_start: 0.8739 (mtp) cc_final: 0.8537 (mtp) REVERT: A 383 ASN cc_start: 0.8012 (t0) cc_final: 0.7608 (t0) REVERT: C 104 MET cc_start: 0.8942 (mtm) cc_final: 0.8704 (mtm) REVERT: E 88 ASN cc_start: 0.7858 (m-40) cc_final: 0.7385 (p0) REVERT: E 90 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8107 (mm-30) REVERT: E 115 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.7823 (m-10) REVERT: I 80 TYR cc_start: 0.8621 (m-80) cc_final: 0.8100 (m-80) REVERT: I 104 MET cc_start: 0.8881 (mtm) cc_final: 0.8671 (mtt) REVERT: I 109 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8155 (pm20) REVERT: K 88 ASN cc_start: 0.7797 (m-40) cc_final: 0.7368 (p0) REVERT: K 90 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8201 (mm-30) REVERT: K 115 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7829 (m-10) REVERT: K 383 ASN cc_start: 0.8056 (t0) cc_final: 0.7632 (t0) outliers start: 44 outliers final: 29 residues processed: 235 average time/residue: 0.2592 time to fit residues: 91.2835 Evaluate side-chains 239 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 205 time to evaluate : 1.775 ------------------------------------------------------------------------------- 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 13 VAL Chi-restraints excluded: chain H residue 22 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 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 22 SER 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 E residue 199 ASN 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 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 187 ASN Chi-restraints excluded: chain K residue 203 SER Chi-restraints excluded: chain K residue 279 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 173 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 111 optimal weight: 0.0980 chunk 154 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.139515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.107455 restraints weight = 17814.986| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.34 r_work: 0.2918 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14859 Z= 0.177 Angle : 0.596 12.431 20205 Z= 0.301 Chirality : 0.042 0.138 2241 Planarity : 0.004 0.042 2592 Dihedral : 5.128 25.078 2322 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.74 % Allowed : 12.91 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.19), residues: 1788 helix: -0.42 (0.35), residues: 222 sheet: -1.04 (0.20), residues: 627 loop : -1.72 (0.18), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 107 HIS 0.003 0.001 HIS A 141 PHE 0.026 0.001 PHE A 440 TYR 0.010 0.001 TYR C 60 ARG 0.006 0.000 ARG E 436 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 15) link_NAG-ASN : angle 2.04551 ( 45) link_BETA1-4 : bond 0.00124 ( 3) link_BETA1-4 : angle 1.61298 ( 9) hydrogen bonds : bond 0.03275 ( 438) hydrogen bonds : angle 5.72831 ( 1197) covalent geometry : bond 0.00427 (14841) covalent geometry : angle 0.58830 (20151) *********************** 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 253 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 210 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 109 GLN cc_start: 0.8562 (pp30) cc_final: 0.8344 (pm20) REVERT: A 88 ASN cc_start: 0.7889 (m-40) cc_final: 0.7489 (p0) REVERT: A 90 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8167 (mm-30) REVERT: A 115 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.7854 (m-10) REVERT: A 317 MET cc_start: 0.8745 (mtp) cc_final: 0.8517 (mtp) REVERT: A 383 ASN cc_start: 0.8035 (t0) cc_final: 0.7652 (t0) REVERT: C 109 GLN cc_start: 0.8591 (pp30) cc_final: 0.8303 (pm20) REVERT: E 88 ASN cc_start: 0.7918 (m-40) cc_final: 0.7469 (p0) REVERT: E 90 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8127 (mm-30) REVERT: E 115 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.7802 (m-10) REVERT: I 80 TYR cc_start: 0.8657 (m-80) cc_final: 0.8142 (m-80) REVERT: I 109 GLN cc_start: 0.8655 (pp30) cc_final: 0.8369 (pm20) REVERT: K 46 CYS cc_start: 0.8639 (m) cc_final: 0.8427 (m) REVERT: K 88 ASN cc_start: 0.7837 (m-40) cc_final: 0.7397 (p0) REVERT: K 90 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8208 (mm-30) REVERT: K 115 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7830 (m-10) REVERT: K 171 ASN cc_start: 0.7603 (m-40) cc_final: 0.7343 (p0) REVERT: K 252 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8784 (mt) REVERT: K 383 ASN cc_start: 0.8082 (t0) cc_final: 0.7662 (t0) REVERT: K 429 LEU cc_start: 0.8911 (tt) cc_final: 0.8704 (tp) outliers start: 43 outliers final: 36 residues processed: 231 average time/residue: 0.2536 time to fit residues: 87.2802 Evaluate side-chains 246 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 1.563 ------------------------------------------------------------------------------- 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 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 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 E residue 199 ASN 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 29 THR Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 115 PHE Chi-restraints excluded: chain K residue 120 ILE 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 203 SER Chi-restraints excluded: chain K residue 252 ILE Chi-restraints excluded: chain K residue 279 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 122 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 176 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 167 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.139295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.107159 restraints weight = 17862.313| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.35 r_work: 0.2961 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 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 0.051 14859 Z= 0.182 Angle : 0.594 13.047 20205 Z= 0.298 Chirality : 0.042 0.137 2241 Planarity : 0.004 0.043 2592 Dihedral : 5.034 25.172 2322 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.31 % Allowed : 14.06 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.19), residues: 1788 helix: -0.29 (0.36), residues: 222 sheet: -0.94 (0.20), residues: 627 loop : -1.62 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.003 0.001 HIS A 141 PHE 0.027 0.001 PHE A 440 TYR 0.010 0.001 TYR C 60 ARG 0.005 0.000 ARG A 436 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 15) link_NAG-ASN : angle 2.03187 ( 45) link_BETA1-4 : bond 0.00117 ( 3) link_BETA1-4 : angle 1.63088 ( 9) hydrogen bonds : bond 0.03231 ( 438) hydrogen bonds : angle 5.64201 ( 1197) covalent geometry : bond 0.00441 (14841) covalent geometry : angle 0.58610 (20151) *********************** 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 265 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 213 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 2 ILE cc_start: 0.8684 (mm) cc_final: 0.8464 (mm) REVERT: A 88 ASN cc_start: 0.7936 (m-40) cc_final: 0.7530 (p0) REVERT: A 90 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8192 (mm-30) REVERT: A 115 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7823 (m-10) REVERT: A 317 MET cc_start: 0.8775 (mtp) cc_final: 0.8529 (mtp) REVERT: A 383 ASN cc_start: 0.8059 (t0) cc_final: 0.7680 (t0) REVERT: C 87 LYS cc_start: 0.6684 (mttm) cc_final: 0.6397 (mttt) REVERT: E 88 ASN cc_start: 0.7935 (m-40) cc_final: 0.7499 (p0) REVERT: E 90 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8184 (mm-30) REVERT: E 115 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7817 (m-10) REVERT: E 442 ASP cc_start: 0.7886 (t70) cc_final: 0.7572 (t0) REVERT: I 80 TYR cc_start: 0.8678 (m-80) cc_final: 0.8164 (m-80) REVERT: I 109 GLN cc_start: 0.8619 (pp30) cc_final: 0.8233 (pm20) REVERT: K 46 CYS cc_start: 0.8638 (m) cc_final: 0.8206 (m) REVERT: K 88 ASN cc_start: 0.7868 (m-40) cc_final: 0.7471 (p0) REVERT: K 90 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8223 (mm-30) REVERT: K 115 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.7811 (m-10) REVERT: K 171 ASN cc_start: 0.7583 (m-40) cc_final: 0.7356 (p0) REVERT: K 252 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.8791 (mt) REVERT: K 383 ASN cc_start: 0.8091 (t0) cc_final: 0.7667 (t0) REVERT: K 429 LEU cc_start: 0.8931 (tt) cc_final: 0.8715 (tp) outliers start: 52 outliers final: 38 residues processed: 242 average time/residue: 0.2409 time to fit residues: 86.9022 Evaluate side-chains 251 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 209 time to evaluate : 1.593 ------------------------------------------------------------------------------- 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 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 120 ILE 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 203 SER 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 106 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 142 ASN E 199 ASN ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 ASN ** K 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.140312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.108558 restraints weight = 17784.032| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.28 r_work: 0.2981 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14859 Z= 0.145 Angle : 0.572 12.393 20205 Z= 0.289 Chirality : 0.041 0.137 2241 Planarity : 0.004 0.044 2592 Dihedral : 4.894 24.580 2322 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.48 % Allowed : 15.59 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.19), residues: 1788 helix: -0.11 (0.36), residues: 222 sheet: -0.83 (0.20), residues: 627 loop : -1.51 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 422 HIS 0.003 0.001 HIS A 141 PHE 0.028 0.001 PHE A 440 TYR 0.011 0.001 TYR C 27 ARG 0.007 0.000 ARG K 436 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 15) link_NAG-ASN : angle 1.96382 ( 45) link_BETA1-4 : bond 0.00131 ( 3) link_BETA1-4 : angle 1.48665 ( 9) hydrogen bonds : bond 0.03060 ( 438) hydrogen bonds : angle 5.51048 ( 1197) covalent geometry : bond 0.00348 (14841) covalent geometry : angle 0.56480 (20151) *********************** 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 254 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 215 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 2 ILE cc_start: 0.8662 (mm) cc_final: 0.8454 (mm) REVERT: A 88 ASN cc_start: 0.7965 (m-40) cc_final: 0.7565 (p0) REVERT: A 90 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8196 (mm-30) REVERT: A 115 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7800 (m-10) REVERT: A 281 LYS cc_start: 0.7989 (mptt) cc_final: 0.7741 (mptt) REVERT: A 317 MET cc_start: 0.8772 (mtp) cc_final: 0.8520 (mtp) REVERT: A 383 ASN cc_start: 0.8042 (t0) cc_final: 0.7664 (t0) REVERT: E 88 ASN cc_start: 0.7932 (m-40) cc_final: 0.7518 (p0) REVERT: E 90 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8176 (mm-30) REVERT: E 115 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7797 (m-10) REVERT: E 442 ASP cc_start: 0.7816 (t70) cc_final: 0.7471 (t0) REVERT: I 80 TYR cc_start: 0.8664 (m-80) cc_final: 0.8154 (m-80) REVERT: I 109 GLN cc_start: 0.8580 (pp30) cc_final: 0.8094 (pm20) REVERT: K 46 CYS cc_start: 0.8491 (m) cc_final: 0.8228 (m) REVERT: K 88 ASN cc_start: 0.7886 (m-40) cc_final: 0.7583 (p0) REVERT: K 90 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8204 (mm-30) REVERT: K 115 PHE cc_start: 0.8321 (OUTLIER) cc_final: 0.7764 (m-10) REVERT: K 276 ASN cc_start: 0.8337 (t0) cc_final: 0.8121 (t0) REVERT: K 383 ASN cc_start: 0.8089 (t0) cc_final: 0.7679 (t0) REVERT: K 429 LEU cc_start: 0.8916 (tt) cc_final: 0.8699 (tp) outliers start: 39 outliers final: 32 residues processed: 230 average time/residue: 0.2737 time to fit residues: 93.8797 Evaluate side-chains 246 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 211 time to evaluate : 1.780 ------------------------------------------------------------------------------- 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 71 SER 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 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 E residue 199 ASN 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 29 THR 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 187 ASN Chi-restraints excluded: chain K residue 203 SER 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 26 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 123 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 ASN ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.139027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.107682 restraints weight = 17834.462| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.17 r_work: 0.2972 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14859 Z= 0.157 Angle : 0.574 12.500 20205 Z= 0.289 Chirality : 0.042 0.137 2241 Planarity : 0.004 0.043 2592 Dihedral : 4.830 24.465 2322 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.67 % Allowed : 15.52 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.19), residues: 1788 helix: 0.03 (0.36), residues: 222 sheet: -0.75 (0.20), residues: 630 loop : -1.46 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 422 HIS 0.003 0.001 HIS A 141 PHE 0.029 0.001 PHE A 440 TYR 0.010 0.001 TYR C 60 ARG 0.007 0.000 ARG K 436 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 15) link_NAG-ASN : angle 1.96626 ( 45) link_BETA1-4 : bond 0.00110 ( 3) link_BETA1-4 : angle 1.50456 ( 9) hydrogen bonds : bond 0.03062 ( 438) hydrogen bonds : angle 5.48040 ( 1197) covalent geometry : bond 0.00379 (14841) covalent geometry : angle 0.56653 (20151) *********************** 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 251 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 209 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASN cc_start: 0.7946 (m-40) cc_final: 0.7566 (p0) REVERT: A 90 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8225 (mm-30) REVERT: A 115 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7793 (m-10) REVERT: A 278 CYS cc_start: 0.8398 (t) cc_final: 0.8023 (p) REVERT: A 317 MET cc_start: 0.8775 (mtp) cc_final: 0.8518 (mtp) REVERT: A 383 ASN cc_start: 0.8050 (t0) cc_final: 0.7670 (t0) REVERT: C 109 GLN cc_start: 0.8508 (pp30) cc_final: 0.8027 (pp30) REVERT: E 88 ASN cc_start: 0.7912 (m-40) cc_final: 0.7697 (p0) REVERT: E 90 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8204 (mm-30) REVERT: E 115 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7777 (m-10) REVERT: E 276 ASN cc_start: 0.8249 (t0) cc_final: 0.8045 (t0) REVERT: E 281 LYS cc_start: 0.8183 (mptt) cc_final: 0.7960 (mptt) REVERT: E 442 ASP cc_start: 0.7822 (t70) cc_final: 0.7482 (t0) REVERT: I 80 TYR cc_start: 0.8667 (m-80) cc_final: 0.8154 (m-80) REVERT: K 46 CYS cc_start: 0.8532 (m) cc_final: 0.8229 (m) REVERT: K 88 ASN cc_start: 0.7909 (m-40) cc_final: 0.7606 (p0) REVERT: K 90 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8197 (mm-30) REVERT: K 115 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7731 (m-10) REVERT: K 383 ASN cc_start: 0.8092 (t0) cc_final: 0.7679 (t0) REVERT: K 429 LEU cc_start: 0.8914 (tt) cc_final: 0.8692 (tp) outliers start: 42 outliers final: 38 residues processed: 228 average time/residue: 0.2637 time to fit residues: 89.4304 Evaluate side-chains 246 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 1.639 ------------------------------------------------------------------------------- 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 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 155 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 199 ASN 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 J residue 79 ILE Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 115 PHE Chi-restraints excluded: chain K residue 120 ILE 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 203 SER 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 119 optimal weight: 0.0020 chunk 51 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 167 optimal weight: 0.6980 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 199 ASN ** 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 = 0.3630 r_free = 0.3630 target = 0.141541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.110846 restraints weight = 17712.864| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.29 r_work: 0.2978 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14859 Z= 0.116 Angle : 0.546 11.391 20205 Z= 0.277 Chirality : 0.041 0.157 2241 Planarity : 0.004 0.041 2592 Dihedral : 4.653 24.051 2322 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.23 % Allowed : 16.35 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.19), residues: 1788 helix: 0.23 (0.36), residues: 222 sheet: -0.66 (0.20), residues: 636 loop : -1.47 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 422 HIS 0.002 0.001 HIS A 141 PHE 0.029 0.001 PHE A 440 TYR 0.014 0.001 TYR F 27 ARG 0.007 0.000 ARG K 436 Details of bonding type rmsd link_NAG-ASN : bond 0.00223 ( 15) link_NAG-ASN : angle 1.90293 ( 45) link_BETA1-4 : bond 0.00186 ( 3) link_BETA1-4 : angle 1.36016 ( 9) hydrogen bonds : bond 0.02850 ( 438) hydrogen bonds : angle 5.34497 ( 1197) covalent geometry : bond 0.00274 (14841) covalent geometry : angle 0.53803 (20151) *********************** 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 239 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 204 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASN cc_start: 0.7945 (m-40) cc_final: 0.7625 (p0) REVERT: A 90 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8245 (mm-30) REVERT: A 115 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7801 (m-10) REVERT: A 278 CYS cc_start: 0.8311 (t) cc_final: 0.7912 (p) REVERT: A 317 MET cc_start: 0.8791 (mtp) cc_final: 0.8542 (mtp) REVERT: A 383 ASN cc_start: 0.8051 (t0) cc_final: 0.7677 (t0) REVERT: C 109 GLN cc_start: 0.8540 (pp30) cc_final: 0.8123 (pp30) REVERT: E 90 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8213 (mm-30) REVERT: E 115 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7725 (m-10) REVERT: E 276 ASN cc_start: 0.8282 (t0) cc_final: 0.8029 (t0) REVERT: E 442 ASP cc_start: 0.7833 (t70) cc_final: 0.7494 (t0) REVERT: I 80 TYR cc_start: 0.8668 (m-80) cc_final: 0.8083 (m-80) REVERT: K 46 CYS cc_start: 0.8542 (m) cc_final: 0.8211 (m) REVERT: K 88 ASN cc_start: 0.7908 (m-40) cc_final: 0.7674 (p0) REVERT: K 90 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8231 (mm-30) REVERT: K 115 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7766 (m-10) REVERT: K 383 ASN cc_start: 0.8063 (t0) cc_final: 0.7669 (t0) REVERT: K 429 LEU cc_start: 0.8951 (tt) cc_final: 0.8740 (tp) outliers start: 35 outliers final: 29 residues processed: 217 average time/residue: 0.2653 time to fit residues: 85.3724 Evaluate side-chains 235 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 71 SER 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 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 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 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 E residue 199 ASN 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 29 THR 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 203 SER 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 129 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 168 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 146 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 199 ASN ** 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 = 0.3610 r_free = 0.3610 target = 0.140049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.108707 restraints weight = 17807.670| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.19 r_work: 0.3006 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14859 Z= 0.141 Angle : 0.563 11.684 20205 Z= 0.284 Chirality : 0.041 0.143 2241 Planarity : 0.004 0.039 2592 Dihedral : 4.645 23.917 2322 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.29 % Allowed : 16.09 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.19), residues: 1788 helix: 0.31 (0.36), residues: 222 sheet: -0.61 (0.20), residues: 636 loop : -1.43 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 422 HIS 0.006 0.001 HIS K 141 PHE 0.030 0.001 PHE A 440 TYR 0.012 0.001 TYR F 27 ARG 0.007 0.000 ARG E 436 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 15) link_NAG-ASN : angle 1.90453 ( 45) link_BETA1-4 : bond 0.00157 ( 3) link_BETA1-4 : angle 1.41075 ( 9) hydrogen bonds : bond 0.02929 ( 438) hydrogen bonds : angle 5.38979 ( 1197) covalent geometry : bond 0.00337 (14841) covalent geometry : angle 0.55528 (20151) ********************** 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 233 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 197 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASN cc_start: 0.7955 (m-40) cc_final: 0.7627 (p0) REVERT: A 90 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8230 (mm-30) REVERT: A 115 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7782 (m-10) REVERT: A 278 CYS cc_start: 0.8290 (t) cc_final: 0.7872 (p) REVERT: A 317 MET cc_start: 0.8769 (mtp) cc_final: 0.8511 (mtp) REVERT: A 383 ASN cc_start: 0.8021 (t0) cc_final: 0.7656 (t0) REVERT: C 109 GLN cc_start: 0.8500 (pp30) cc_final: 0.8068 (pp30) REVERT: E 90 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8199 (mm-30) REVERT: E 115 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7697 (m-10) REVERT: E 276 ASN cc_start: 0.8234 (t0) cc_final: 0.8023 (t0) REVERT: E 292 SER cc_start: 0.9121 (t) cc_final: 0.8886 (p) REVERT: E 442 ASP cc_start: 0.7829 (t70) cc_final: 0.7494 (t0) REVERT: I 80 TYR cc_start: 0.8665 (m-80) cc_final: 0.8157 (m-80) REVERT: K 46 CYS cc_start: 0.8496 (m) cc_final: 0.8183 (m) REVERT: K 88 ASN cc_start: 0.7938 (m-40) cc_final: 0.7699 (p0) REVERT: K 90 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8253 (mm-30) REVERT: K 115 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7739 (m-10) REVERT: K 383 ASN cc_start: 0.8063 (t0) cc_final: 0.7660 (t0) REVERT: K 429 LEU cc_start: 0.8929 (tt) cc_final: 0.8717 (tp) outliers start: 36 outliers final: 28 residues processed: 211 average time/residue: 0.2529 time to fit residues: 79.6827 Evaluate side-chains 226 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 71 SER 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 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 71 SER 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 155 THR Chi-restraints excluded: chain E residue 160 LEU 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 29 THR 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 187 ASN Chi-restraints excluded: chain K residue 203 SER 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 91 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 199 ASN ** 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 = 0.3653 r_free = 0.3653 target = 0.142713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.111256 restraints weight = 17766.271| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.22 r_work: 0.3096 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14859 Z= 0.155 Angle : 0.568 12.091 20205 Z= 0.287 Chirality : 0.041 0.138 2241 Planarity : 0.004 0.039 2592 Dihedral : 4.656 24.130 2322 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.42 % Allowed : 16.22 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.19), residues: 1788 helix: 0.33 (0.36), residues: 222 sheet: -0.57 (0.20), residues: 636 loop : -1.40 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 422 HIS 0.003 0.001 HIS A 141 PHE 0.031 0.001 PHE A 440 TYR 0.010 0.001 TYR F 27 ARG 0.007 0.000 ARG E 436 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 15) link_NAG-ASN : angle 1.90276 ( 45) link_BETA1-4 : bond 0.00141 ( 3) link_BETA1-4 : angle 1.42799 ( 9) hydrogen bonds : bond 0.02971 ( 438) hydrogen bonds : angle 5.41369 ( 1197) covalent geometry : bond 0.00374 (14841) covalent geometry : angle 0.56100 (20151) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8957.38 seconds wall clock time: 155 minutes 32.76 seconds (9332.76 seconds total)