Starting phenix.real_space_refine on Fri Sep 27 01:13:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhk_33831/09_2024/7yhk_33831.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhk_33831/09_2024/7yhk_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhk_33831/09_2024/7yhk_33831.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhk_33831/09_2024/7yhk_33831.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhk_33831/09_2024/7yhk_33831.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhk_33831/09_2024/7yhk_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 8.37, per 1000 atoms: 0.58 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: 3.12 Conformation dependent library (CDL) restraints added in 1.7 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: 2.09 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: 5.64 Time building geometry restraints manager: 3.75 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } 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: 9.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.080 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.380 ------------------------------------------------------------------------------- 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 14841 Z= 0.447 Angle : 0.995 13.371 20151 Z= 0.577 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 *********************** 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 fitting. rotamer outliers: 12 poor density : 270 time to evaluate : 1.598 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: 0.2649 time to fit residues: 107.6056 Evaluate side-chains 213 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 208 time to evaluate : 1.462 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 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 14841 Z= 0.219 Angle : 0.612 8.441 20151 Z= 0.319 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 *********************** 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 fitting. rotamer outliers: 21 poor density : 243 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 2 ILE cc_start: 0.8171 (mm) cc_final: 0.7909 (mm) REVERT: F 87 LYS cc_start: 0.6107 (mttm) cc_final: 0.5873 (mttt) REVERT: A 46 CYS cc_start: 0.8308 (m) cc_final: 0.8055 (m) REVERT: A 55 GLN cc_start: 0.8503 (tt0) cc_final: 0.8294 (mt0) REVERT: A 72 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7485 (mt-10) REVERT: A 88 ASN cc_start: 0.7754 (m-40) cc_final: 0.6938 (p0) REVERT: A 90 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7305 (mm-30) REVERT: A 219 LYS cc_start: 0.8216 (tttm) cc_final: 0.7704 (ttmt) REVERT: A 275 MET cc_start: 0.7964 (tpt) cc_final: 0.7504 (tpt) REVERT: A 316 ARG cc_start: 0.7893 (mtp85) cc_final: 0.7623 (mtt90) REVERT: A 317 MET cc_start: 0.7872 (mtp) cc_final: 0.7398 (tpp) REVERT: A 383 ASN cc_start: 0.6646 (t0) cc_final: 0.6216 (t0) REVERT: A 402 LYS cc_start: 0.7508 (mmtm) cc_final: 0.7133 (mmmt) REVERT: A 407 MET cc_start: 0.6620 (ttp) cc_final: 0.6248 (ttp) REVERT: E 44 LYS cc_start: 0.6704 (mtmt) cc_final: 0.6248 (mtpt) REVERT: E 88 ASN cc_start: 0.7672 (m-40) cc_final: 0.6825 (p0) REVERT: E 90 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7298 (mm-30) REVERT: E 156 GLU cc_start: 0.8210 (pt0) cc_final: 0.7984 (pt0) REVERT: E 219 LYS cc_start: 0.8241 (tttm) cc_final: 0.7727 (ttmt) REVERT: E 276 ASN cc_start: 0.7625 (t0) cc_final: 0.7342 (t0) REVERT: E 402 LYS cc_start: 0.7341 (mmpt) cc_final: 0.7017 (mtpt) REVERT: E 407 MET cc_start: 0.6683 (ttp) cc_final: 0.6428 (ttp) REVERT: I 54 TYR cc_start: 0.7367 (t80) cc_final: 0.7084 (t80) REVERT: I 82 GLN cc_start: 0.7008 (tt0) cc_final: 0.6716 (tt0) REVERT: K 88 ASN cc_start: 0.7708 (m-40) cc_final: 0.6957 (p0) REVERT: K 90 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7413 (mm-30) REVERT: K 156 GLU cc_start: 0.8147 (pt0) cc_final: 0.7847 (pt0) REVERT: K 219 LYS cc_start: 0.8308 (tttm) cc_final: 0.7796 (ttmt) REVERT: K 275 MET cc_start: 0.8026 (tpt) cc_final: 0.7376 (tpt) REVERT: K 276 ASN cc_start: 0.7277 (t0) cc_final: 0.6691 (t0) REVERT: K 316 ARG cc_start: 0.7868 (mtp85) cc_final: 0.7612 (mtt90) REVERT: K 317 MET cc_start: 0.7964 (mtp) cc_final: 0.7713 (mtp) REVERT: K 383 ASN cc_start: 0.6720 (t0) cc_final: 0.6284 (t0) outliers start: 21 outliers final: 20 residues processed: 252 average time/residue: 0.2965 time to fit residues: 107.5463 Evaluate side-chains 247 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 227 time to evaluate : 1.722 ------------------------------------------------------------------------------- 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 89 optimal weight: 0.3980 chunk 49 optimal weight: 4.9990 chunk 133 optimal weight: 0.0570 chunk 109 optimal weight: 0.4980 chunk 44 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN A 199 ASN A 226 GLN C 109 GLN D 78 ASN E 55 GLN I 109 GLN ** K 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14841 Z= 0.172 Angle : 0.549 8.688 20151 Z= 0.284 Chirality : 0.041 0.136 2241 Planarity : 0.004 0.042 2592 Dihedral : 5.050 24.434 2323 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.59 % Allowed : 10.81 % Favored : 87.60 % 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: -2.38 (0.18), residues: 1788 helix: -0.83 (0.34), residues: 222 sheet: -1.32 (0.20), residues: 588 loop : -1.92 (0.17), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 107 HIS 0.002 0.001 HIS E 184 PHE 0.012 0.001 PHE K 440 TYR 0.010 0.001 TYR F 80 ARG 0.005 0.000 ARG K 436 *********************** 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 255 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 230 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2 ILE cc_start: 0.8118 (mm) cc_final: 0.7861 (mm) REVERT: F 109 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7343 (pp30) REVERT: H 23 CYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8325 (t) REVERT: A 46 CYS cc_start: 0.8305 (m) cc_final: 0.8080 (m) REVERT: A 55 GLN cc_start: 0.8502 (tt0) cc_final: 0.8272 (mt0) REVERT: A 72 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7461 (mt-10) REVERT: A 88 ASN cc_start: 0.7765 (m-40) cc_final: 0.6993 (p0) REVERT: A 90 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7328 (mm-30) REVERT: A 115 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7343 (m-10) REVERT: A 219 LYS cc_start: 0.8187 (tttm) cc_final: 0.7688 (ttmt) REVERT: A 275 MET cc_start: 0.8005 (tpt) cc_final: 0.7436 (tpt) REVERT: A 276 ASN cc_start: 0.7729 (t0) cc_final: 0.7355 (t0) REVERT: A 316 ARG cc_start: 0.7888 (mtp85) cc_final: 0.7507 (ttt90) REVERT: A 317 MET cc_start: 0.7901 (mtp) cc_final: 0.7389 (tpp) REVERT: A 383 ASN cc_start: 0.6605 (t0) cc_final: 0.6210 (t0) REVERT: A 398 LYS cc_start: 0.8323 (mttm) cc_final: 0.7930 (mtpp) REVERT: A 402 LYS cc_start: 0.7395 (mmtm) cc_final: 0.7075 (mmmt) REVERT: C 104 MET cc_start: 0.8146 (mtm) cc_final: 0.7865 (mtt) REVERT: C 109 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7038 (pp30) REVERT: E 44 LYS cc_start: 0.6490 (mtmt) cc_final: 0.6025 (mtpt) REVERT: E 88 ASN cc_start: 0.7716 (m-40) cc_final: 0.7222 (p0) REVERT: E 90 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7300 (mm-30) REVERT: E 115 PHE cc_start: 0.7844 (OUTLIER) cc_final: 0.7259 (m-10) REVERT: E 219 LYS cc_start: 0.8194 (tttm) cc_final: 0.7703 (ttmt) REVERT: E 276 ASN cc_start: 0.7725 (t0) cc_final: 0.7335 (t0) REVERT: E 402 LYS cc_start: 0.7323 (mmpt) cc_final: 0.7033 (mtpt) REVERT: E 407 MET cc_start: 0.6678 (ttp) cc_final: 0.6452 (ttp) REVERT: I 54 TYR cc_start: 0.7240 (t80) cc_final: 0.6967 (t80) REVERT: I 82 GLN cc_start: 0.7017 (tt0) cc_final: 0.6719 (tt0) REVERT: J 23 CYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8597 (t) REVERT: K 88 ASN cc_start: 0.7727 (m-40) cc_final: 0.6930 (p0) REVERT: K 90 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7481 (mm-30) REVERT: K 115 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.7278 (m-10) REVERT: K 219 LYS cc_start: 0.8270 (tttm) cc_final: 0.7728 (ttmt) REVERT: K 317 MET cc_start: 0.7910 (mtp) cc_final: 0.7641 (mtp) REVERT: K 383 ASN cc_start: 0.6678 (t0) cc_final: 0.6240 (t0) outliers start: 25 outliers final: 13 residues processed: 238 average time/residue: 0.2886 time to fit residues: 98.9978 Evaluate side-chains 236 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 216 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain H residue 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 199 ASN Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 115 PHE Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 187 ASN Chi-restraints excluded: chain K residue 203 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 0.5980 chunk 121 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 H 6 GLN A 199 ASN C 109 GLN D 78 ASN E 142 ASN E 196 HIS I 6 GLN I 109 GLN J 6 GLN K 142 ASN K 196 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 14841 Z= 0.387 Angle : 0.641 11.823 20151 Z= 0.325 Chirality : 0.044 0.134 2241 Planarity : 0.004 0.043 2592 Dihedral : 5.218 25.669 2322 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.86 % Allowed : 10.62 % Favored : 86.51 % 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: -2.16 (0.18), residues: 1788 helix: -0.59 (0.35), residues: 222 sheet: -1.14 (0.20), residues: 627 loop : -1.83 (0.18), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 107 HIS 0.005 0.001 HIS K 184 PHE 0.025 0.002 PHE A 440 TYR 0.012 0.002 TYR J 36 ARG 0.005 0.001 ARG K 220 *********************** 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 263 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 218 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2 ILE cc_start: 0.8181 (mm) cc_final: 0.7900 (mm) REVERT: F 109 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7523 (pm20) REVERT: H 23 CYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8445 (t) REVERT: A 46 CYS cc_start: 0.8497 (m) cc_final: 0.8255 (m) REVERT: A 72 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7509 (mt-10) REVERT: A 90 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7549 (mm-30) REVERT: A 115 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7348 (m-10) REVERT: A 219 LYS cc_start: 0.8207 (tttm) cc_final: 0.7721 (tttp) REVERT: A 275 MET cc_start: 0.7897 (tpt) cc_final: 0.7305 (tpt) REVERT: A 276 ASN cc_start: 0.7675 (t0) cc_final: 0.7400 (t0) REVERT: A 317 MET cc_start: 0.8029 (mtp) cc_final: 0.7492 (mtp) REVERT: A 383 ASN cc_start: 0.6660 (t0) cc_final: 0.6244 (t0) REVERT: A 402 LYS cc_start: 0.7375 (mmtm) cc_final: 0.7167 (mtpt) REVERT: C 104 MET cc_start: 0.8362 (mtm) cc_final: 0.8156 (mtt) REVERT: E 90 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7418 (mm-30) REVERT: E 115 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7387 (m-10) REVERT: E 219 LYS cc_start: 0.8191 (tttm) cc_final: 0.7689 (ttmt) REVERT: E 402 LYS cc_start: 0.7191 (mmpt) cc_final: 0.6928 (mtpt) REVERT: I 54 TYR cc_start: 0.7224 (t80) cc_final: 0.6980 (t80) REVERT: I 80 TYR cc_start: 0.7616 (m-80) cc_final: 0.7129 (m-80) REVERT: I 104 MET cc_start: 0.8344 (mtm) cc_final: 0.8020 (mtt) REVERT: J 23 CYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8372 (t) REVERT: K 46 CYS cc_start: 0.8485 (m) cc_final: 0.8193 (m) REVERT: K 90 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7593 (mm-30) REVERT: K 115 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7299 (m-10) REVERT: K 219 LYS cc_start: 0.8207 (tttm) cc_final: 0.7638 (ttmm) REVERT: K 252 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7381 (mt) REVERT: K 276 ASN cc_start: 0.7618 (t0) cc_final: 0.7333 (t0) REVERT: K 383 ASN cc_start: 0.6756 (t0) cc_final: 0.6311 (t0) outliers start: 45 outliers final: 32 residues processed: 241 average time/residue: 0.2605 time to fit residues: 91.9136 Evaluate side-chains 251 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 212 time to evaluate : 1.449 ------------------------------------------------------------------------------- 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 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 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 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 142 ASN Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 58 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 145 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 6 GLN A 199 ASN I 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14841 Z= 0.210 Angle : 0.558 11.379 20151 Z= 0.284 Chirality : 0.041 0.134 2241 Planarity : 0.004 0.040 2592 Dihedral : 4.954 24.906 2322 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.29 % Allowed : 12.40 % 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: -1.93 (0.19), residues: 1788 helix: -0.28 (0.36), residues: 222 sheet: -1.03 (0.20), residues: 597 loop : -1.68 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 107 HIS 0.002 0.001 HIS K 184 PHE 0.026 0.001 PHE A 440 TYR 0.009 0.001 TYR C 60 ARG 0.006 0.000 ARG E 436 *********************** 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 256 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 220 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2 ILE cc_start: 0.8152 (mm) cc_final: 0.7882 (mm) REVERT: H 23 CYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8535 (t) REVERT: A 46 CYS cc_start: 0.8386 (m) cc_final: 0.7996 (m) REVERT: A 72 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7488 (mt-10) REVERT: A 88 ASN cc_start: 0.7768 (m-40) cc_final: 0.7017 (p0) REVERT: A 90 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7550 (mm-30) REVERT: A 115 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7320 (m-10) REVERT: A 219 LYS cc_start: 0.8202 (tttm) cc_final: 0.7722 (tttp) REVERT: A 276 ASN cc_start: 0.7583 (t0) cc_final: 0.7314 (t0) REVERT: A 316 ARG cc_start: 0.7882 (mtp85) cc_final: 0.7591 (ttt90) REVERT: A 317 MET cc_start: 0.8066 (mtp) cc_final: 0.7522 (mtp) REVERT: A 383 ASN cc_start: 0.6637 (t0) cc_final: 0.6229 (t0) REVERT: C 104 MET cc_start: 0.8260 (mtm) cc_final: 0.8036 (mtm) REVERT: C 109 GLN cc_start: 0.7859 (pp30) cc_final: 0.7565 (pm20) REVERT: E 88 ASN cc_start: 0.7751 (m-40) cc_final: 0.7255 (p0) REVERT: E 90 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7470 (mm-30) REVERT: E 115 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.7245 (m-10) REVERT: E 219 LYS cc_start: 0.8182 (tttm) cc_final: 0.7688 (ttmt) REVERT: E 402 LYS cc_start: 0.7049 (mmpt) cc_final: 0.6847 (mtpt) REVERT: I 54 TYR cc_start: 0.7163 (t80) cc_final: 0.6893 (t80) REVERT: I 80 TYR cc_start: 0.7635 (m-80) cc_final: 0.7082 (m-80) REVERT: I 104 MET cc_start: 0.8191 (mtm) cc_final: 0.7869 (mtt) REVERT: I 109 GLN cc_start: 0.7986 (pp30) cc_final: 0.7673 (pm20) REVERT: J 23 CYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8453 (t) REVERT: K 88 ASN cc_start: 0.7761 (m-40) cc_final: 0.6945 (p0) REVERT: K 90 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7600 (mm-30) REVERT: K 115 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7236 (m-10) REVERT: K 171 ASN cc_start: 0.6497 (m-40) cc_final: 0.6150 (p0) REVERT: K 219 LYS cc_start: 0.8223 (tttm) cc_final: 0.7657 (ttmm) REVERT: K 383 ASN cc_start: 0.6744 (t0) cc_final: 0.6308 (t0) outliers start: 36 outliers final: 25 residues processed: 240 average time/residue: 0.2674 time to fit residues: 93.9436 Evaluate side-chains 244 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 214 time to evaluate : 1.819 ------------------------------------------------------------------------------- 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 23 CYS 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 58 LEU Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 23 CYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 171 optimal weight: 0.8980 chunk 142 optimal weight: 0.3980 chunk 79 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 6 GLN D 6 GLN I 6 GLN K 142 ASN ** K 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14841 Z= 0.203 Angle : 0.544 11.306 20151 Z= 0.277 Chirality : 0.041 0.134 2241 Planarity : 0.004 0.041 2592 Dihedral : 4.743 24.429 2322 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.80 % Allowed : 12.53 % Favored : 84.67 % 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: -1.71 (0.19), residues: 1788 helix: -0.09 (0.36), residues: 222 sheet: -0.89 (0.20), residues: 597 loop : -1.53 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 422 HIS 0.003 0.001 HIS K 184 PHE 0.027 0.001 PHE A 440 TYR 0.009 0.001 TYR C 60 ARG 0.005 0.000 ARG E 436 *********************** 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 261 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 217 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2 ILE cc_start: 0.8135 (mm) cc_final: 0.7862 (mm) REVERT: F 109 GLN cc_start: 0.7865 (pp30) cc_final: 0.7628 (pm20) REVERT: H 23 CYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8549 (t) REVERT: A 46 CYS cc_start: 0.8198 (m) cc_final: 0.7905 (m) REVERT: A 72 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7506 (mt-10) REVERT: A 88 ASN cc_start: 0.7772 (m-40) cc_final: 0.7036 (p0) REVERT: A 90 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7572 (mm-30) REVERT: A 115 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.7253 (m-10) REVERT: A 219 LYS cc_start: 0.8221 (tttm) cc_final: 0.7733 (tttp) REVERT: A 276 ASN cc_start: 0.7433 (t0) cc_final: 0.7184 (t0) REVERT: A 316 ARG cc_start: 0.7864 (mtp85) cc_final: 0.7594 (ttt90) REVERT: A 317 MET cc_start: 0.8075 (mtp) cc_final: 0.7526 (mtp) REVERT: A 383 ASN cc_start: 0.6612 (t0) cc_final: 0.6204 (t0) REVERT: C 109 GLN cc_start: 0.7786 (pp30) cc_final: 0.7460 (pm20) REVERT: E 88 ASN cc_start: 0.7769 (m-40) cc_final: 0.7287 (p0) REVERT: E 90 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7511 (mm-30) REVERT: E 115 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.7260 (m-10) REVERT: E 171 ASN cc_start: 0.6500 (m-40) cc_final: 0.6146 (p0) REVERT: E 219 LYS cc_start: 0.8188 (tttm) cc_final: 0.7697 (ttmt) REVERT: E 402 LYS cc_start: 0.7049 (mmpt) cc_final: 0.6835 (mtpt) REVERT: I 2 ILE cc_start: 0.8186 (mm) cc_final: 0.7901 (mm) REVERT: I 80 TYR cc_start: 0.7624 (m-80) cc_final: 0.6959 (m-80) REVERT: I 104 MET cc_start: 0.8140 (mtm) cc_final: 0.7840 (mtt) REVERT: I 109 GLN cc_start: 0.7917 (pp30) cc_final: 0.7577 (pm20) REVERT: J 23 CYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8521 (t) REVERT: K 46 CYS cc_start: 0.8399 (m) cc_final: 0.7811 (m) REVERT: K 88 ASN cc_start: 0.7755 (m-40) cc_final: 0.7012 (p0) REVERT: K 90 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7598 (mm-30) REVERT: K 115 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7200 (m-10) REVERT: K 171 ASN cc_start: 0.6493 (m-40) cc_final: 0.6157 (p0) REVERT: K 219 LYS cc_start: 0.8179 (tttm) cc_final: 0.7623 (ttmm) REVERT: K 276 ASN cc_start: 0.7607 (t0) cc_final: 0.7380 (t0) REVERT: K 383 ASN cc_start: 0.6725 (t0) cc_final: 0.6297 (t0) outliers start: 44 outliers final: 30 residues processed: 241 average time/residue: 0.2658 time to fit residues: 93.2622 Evaluate side-chains 249 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 214 time to evaluate : 1.542 ------------------------------------------------------------------------------- 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 23 CYS 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 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 115 PHE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 115 PHE Chi-restraints excluded: chain K residue 142 ASN Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 187 ASN Chi-restraints excluded: chain K residue 203 SER 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 165 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN A 199 ASN C 6 GLN C 109 GLN E 142 ASN I 109 GLN K 142 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 14841 Z= 0.386 Angle : 0.638 14.838 20151 Z= 0.321 Chirality : 0.044 0.145 2241 Planarity : 0.004 0.045 2592 Dihedral : 5.074 25.463 2322 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.18 % Allowed : 13.42 % Favored : 83.40 % 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: -1.69 (0.19), residues: 1788 helix: -0.20 (0.36), residues: 222 sheet: -0.79 (0.20), residues: 627 loop : -1.56 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 64 HIS 0.004 0.001 HIS K 184 PHE 0.030 0.002 PHE A 440 TYR 0.012 0.002 TYR J 34 ARG 0.007 0.001 ARG K 436 *********************** 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 269 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 219 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 2 ILE cc_start: 0.8175 (mm) cc_final: 0.7900 (mm) REVERT: F 109 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7383 (pm20) REVERT: H 23 CYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8558 (t) REVERT: A 46 CYS cc_start: 0.8193 (m) cc_final: 0.7880 (m) REVERT: A 72 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7520 (mt-10) REVERT: A 88 ASN cc_start: 0.7787 (m-40) cc_final: 0.7057 (p0) REVERT: A 90 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7628 (mm-30) REVERT: A 115 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7334 (m-10) REVERT: A 219 LYS cc_start: 0.8266 (tttm) cc_final: 0.7771 (tttp) REVERT: A 276 ASN cc_start: 0.7409 (t0) cc_final: 0.7188 (t0) REVERT: A 317 MET cc_start: 0.8116 (mtp) cc_final: 0.7542 (mtp) REVERT: A 383 ASN cc_start: 0.6690 (t0) cc_final: 0.6255 (t0) REVERT: C 2 ILE cc_start: 0.8185 (mm) cc_final: 0.7916 (mm) REVERT: E 88 ASN cc_start: 0.7799 (m-40) cc_final: 0.7096 (p0) REVERT: E 90 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7614 (mm-30) REVERT: E 115 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7367 (m-10) REVERT: E 171 ASN cc_start: 0.6487 (m-40) cc_final: 0.6121 (p0) REVERT: E 219 LYS cc_start: 0.8197 (tttm) cc_final: 0.7681 (ttmt) REVERT: E 402 LYS cc_start: 0.7061 (mmpt) cc_final: 0.6808 (mtpt) REVERT: E 442 ASP cc_start: 0.7407 (t70) cc_final: 0.7161 (t0) REVERT: I 80 TYR cc_start: 0.7673 (m-80) cc_final: 0.7094 (m-80) REVERT: I 104 MET cc_start: 0.8310 (mtm) cc_final: 0.8061 (mtt) REVERT: J 23 CYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8466 (t) REVERT: K 46 CYS cc_start: 0.8253 (m) cc_final: 0.7829 (m) REVERT: K 88 ASN cc_start: 0.7856 (m-40) cc_final: 0.7127 (p0) REVERT: K 90 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7622 (mm-30) REVERT: K 115 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.7308 (m-10) REVERT: K 171 ASN cc_start: 0.6555 (m-40) cc_final: 0.6195 (p0) REVERT: K 219 LYS cc_start: 0.8204 (tttm) cc_final: 0.7622 (ttmm) REVERT: K 252 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7417 (mt) REVERT: K 276 ASN cc_start: 0.7577 (t0) cc_final: 0.7325 (t0) REVERT: K 383 ASN cc_start: 0.6796 (t0) cc_final: 0.6366 (t0) outliers start: 50 outliers final: 40 residues processed: 239 average time/residue: 0.2738 time to fit residues: 95.2670 Evaluate side-chains 267 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 220 time to evaluate : 1.641 ------------------------------------------------------------------------------- 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 H residue 23 CYS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 115 PHE Chi-restraints excluded: chain K residue 142 ASN Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 187 ASN Chi-restraints excluded: chain K residue 203 SER Chi-restraints excluded: chain K residue 252 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 51 optimal weight: 0.0980 chunk 33 optimal weight: 0.0670 chunk 108 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 ASN C 6 GLN ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14841 Z= 0.159 Angle : 0.532 11.455 20151 Z= 0.273 Chirality : 0.041 0.139 2241 Planarity : 0.004 0.040 2592 Dihedral : 4.687 24.248 2322 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.16 % Allowed : 15.01 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.53 (0.19), residues: 1788 helix: 0.20 (0.36), residues: 222 sheet: -0.73 (0.20), residues: 609 loop : -1.49 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 107 HIS 0.004 0.001 HIS E 141 PHE 0.029 0.001 PHE A 440 TYR 0.009 0.001 TYR C 60 ARG 0.007 0.000 ARG K 436 *********************** 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 254 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 220 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2 ILE cc_start: 0.8144 (mm) cc_final: 0.7880 (mm) REVERT: H 23 CYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8576 (t) REVERT: A 46 CYS cc_start: 0.8112 (m) cc_final: 0.7800 (m) REVERT: A 72 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7462 (mt-10) REVERT: A 88 ASN cc_start: 0.7817 (m-40) cc_final: 0.7097 (p0) REVERT: A 90 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7622 (mm-30) REVERT: A 115 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7221 (m-10) REVERT: A 219 LYS cc_start: 0.8232 (tttm) cc_final: 0.7752 (tttp) REVERT: A 316 ARG cc_start: 0.7861 (mtp85) cc_final: 0.7636 (ttt90) REVERT: A 317 MET cc_start: 0.8104 (mtp) cc_final: 0.7553 (mtp) REVERT: A 383 ASN cc_start: 0.6639 (t0) cc_final: 0.6232 (t0) REVERT: C 2 ILE cc_start: 0.8170 (mm) cc_final: 0.7921 (mm) REVERT: E 88 ASN cc_start: 0.7757 (m-40) cc_final: 0.7112 (p0) REVERT: E 90 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7648 (mm-30) REVERT: E 115 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7250 (m-10) REVERT: E 140 SER cc_start: 0.8101 (p) cc_final: 0.7764 (m) REVERT: E 171 ASN cc_start: 0.6425 (m-40) cc_final: 0.6099 (p0) REVERT: E 219 LYS cc_start: 0.8177 (tttm) cc_final: 0.7674 (ttmt) REVERT: E 402 LYS cc_start: 0.7067 (mmpt) cc_final: 0.6816 (mtpt) REVERT: E 442 ASP cc_start: 0.7411 (t70) cc_final: 0.7155 (t0) REVERT: I 80 TYR cc_start: 0.7656 (m-80) cc_final: 0.7027 (m-80) REVERT: I 104 MET cc_start: 0.8085 (mtm) cc_final: 0.7807 (mtt) REVERT: J 23 CYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8541 (t) REVERT: K 46 CYS cc_start: 0.8228 (m) cc_final: 0.7749 (m) REVERT: K 88 ASN cc_start: 0.7841 (m-40) cc_final: 0.7150 (p0) REVERT: K 90 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7579 (mm-30) REVERT: K 115 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7208 (m-10) REVERT: K 171 ASN cc_start: 0.6516 (m-40) cc_final: 0.6217 (p0) REVERT: K 219 LYS cc_start: 0.8171 (tttm) cc_final: 0.7610 (ttmm) REVERT: K 276 ASN cc_start: 0.7688 (t0) cc_final: 0.7413 (t0) REVERT: K 383 ASN cc_start: 0.6734 (t0) cc_final: 0.6324 (t0) outliers start: 34 outliers final: 26 residues processed: 233 average time/residue: 0.2658 time to fit residues: 90.4305 Evaluate side-chains 247 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 216 time to evaluate : 1.708 ------------------------------------------------------------------------------- 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 23 CYS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain 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 115 PHE 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 71 SER Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 28 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 150 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 168 optimal weight: 0.0870 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 142 ASN ** K 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14841 Z= 0.189 Angle : 0.535 11.449 20151 Z= 0.274 Chirality : 0.041 0.135 2241 Planarity : 0.004 0.039 2592 Dihedral : 4.587 23.849 2322 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.23 % Allowed : 15.33 % Favored : 82.44 % 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: 0.34 (0.37), residues: 222 sheet: -0.61 (0.20), residues: 606 loop : -1.41 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 422 HIS 0.009 0.001 HIS E 141 PHE 0.030 0.001 PHE A 440 TYR 0.009 0.001 TYR C 60 ARG 0.006 0.000 ARG E 436 *********************** 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 249 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 214 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2 ILE cc_start: 0.8163 (mm) cc_final: 0.7914 (mm) REVERT: H 23 CYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8590 (t) REVERT: A 72 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7460 (mt-10) REVERT: A 88 ASN cc_start: 0.7817 (m-40) cc_final: 0.7140 (p0) REVERT: A 90 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7653 (mm-30) REVERT: A 115 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.7247 (m-10) REVERT: A 219 LYS cc_start: 0.8262 (tttm) cc_final: 0.7770 (tttp) REVERT: A 316 ARG cc_start: 0.7828 (mtp85) cc_final: 0.7596 (ttt90) REVERT: A 317 MET cc_start: 0.8101 (mtp) cc_final: 0.7542 (mtp) REVERT: A 383 ASN cc_start: 0.6628 (t0) cc_final: 0.6224 (t0) REVERT: C 2 ILE cc_start: 0.8164 (mm) cc_final: 0.7916 (mm) REVERT: E 88 ASN cc_start: 0.7771 (m-40) cc_final: 0.7345 (p0) REVERT: E 90 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7660 (mm-30) REVERT: E 115 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.7203 (m-10) REVERT: E 171 ASN cc_start: 0.6453 (m-40) cc_final: 0.6128 (p0) REVERT: E 219 LYS cc_start: 0.8179 (tttm) cc_final: 0.7680 (ttmt) REVERT: E 276 ASN cc_start: 0.7723 (t0) cc_final: 0.7480 (t0) REVERT: E 402 LYS cc_start: 0.7029 (mmpt) cc_final: 0.6746 (mtpt) REVERT: E 442 ASP cc_start: 0.7409 (t70) cc_final: 0.7158 (t0) REVERT: I 80 TYR cc_start: 0.7664 (m-80) cc_final: 0.7029 (m-80) REVERT: I 104 MET cc_start: 0.8104 (mtm) cc_final: 0.7839 (mtt) REVERT: J 23 CYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8580 (t) REVERT: K 46 CYS cc_start: 0.8215 (m) cc_final: 0.7706 (m) REVERT: K 88 ASN cc_start: 0.7895 (m-40) cc_final: 0.7226 (p0) REVERT: K 90 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7596 (mm-30) REVERT: K 115 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.7188 (m-10) REVERT: K 140 SER cc_start: 0.8129 (p) cc_final: 0.7738 (m) REVERT: K 171 ASN cc_start: 0.6538 (m-40) cc_final: 0.6248 (p0) REVERT: K 219 LYS cc_start: 0.8173 (tttm) cc_final: 0.7614 (ttmm) REVERT: K 276 ASN cc_start: 0.7655 (t0) cc_final: 0.7383 (t0) REVERT: K 383 ASN cc_start: 0.6755 (t0) cc_final: 0.6333 (t0) outliers start: 35 outliers final: 26 residues processed: 229 average time/residue: 0.3256 time to fit residues: 109.3891 Evaluate side-chains 243 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 212 time to evaluate : 1.655 ------------------------------------------------------------------------------- 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 23 CYS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain C residue 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 155 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 199 ASN 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 23 CYS Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 115 PHE 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 102 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 176 optimal weight: 7.9990 chunk 162 optimal weight: 0.5980 chunk 140 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 14841 Z= 0.246 Angle : 0.762 59.181 20151 Z= 0.430 Chirality : 0.041 0.197 2241 Planarity : 0.004 0.067 2592 Dihedral : 4.628 29.219 2322 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.04 % Allowed : 15.46 % Favored : 82.51 % 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: -1.37 (0.19), residues: 1788 helix: 0.35 (0.37), residues: 222 sheet: -0.60 (0.20), residues: 606 loop : -1.41 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 422 HIS 0.005 0.001 HIS E 141 PHE 0.028 0.001 PHE A 440 TYR 0.009 0.001 TYR C 60 ARG 0.008 0.000 ARG E 436 ********************** 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 244 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 212 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2 ILE cc_start: 0.8164 (mm) cc_final: 0.7915 (mm) REVERT: H 23 CYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8591 (t) REVERT: A 72 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7457 (mt-10) REVERT: A 88 ASN cc_start: 0.7818 (m-40) cc_final: 0.7140 (p0) REVERT: A 90 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7654 (mm-30) REVERT: A 115 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.7247 (m-10) REVERT: A 219 LYS cc_start: 0.8262 (tttm) cc_final: 0.7771 (tttp) REVERT: A 316 ARG cc_start: 0.7829 (mtp85) cc_final: 0.7598 (ttt90) REVERT: A 317 MET cc_start: 0.8101 (mtp) cc_final: 0.7541 (mtp) REVERT: A 383 ASN cc_start: 0.6629 (t0) cc_final: 0.6224 (t0) REVERT: C 2 ILE cc_start: 0.8164 (mm) cc_final: 0.7917 (mm) REVERT: E 88 ASN cc_start: 0.7771 (m-40) cc_final: 0.7345 (p0) REVERT: E 90 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7661 (mm-30) REVERT: E 115 PHE cc_start: 0.7791 (OUTLIER) cc_final: 0.7204 (m-10) REVERT: E 171 ASN cc_start: 0.6455 (m-40) cc_final: 0.6129 (p0) REVERT: E 219 LYS cc_start: 0.8179 (tttm) cc_final: 0.7680 (ttmt) REVERT: E 276 ASN cc_start: 0.7721 (t0) cc_final: 0.7481 (t0) REVERT: E 402 LYS cc_start: 0.7030 (mmpt) cc_final: 0.6747 (mtpt) REVERT: E 442 ASP cc_start: 0.7410 (t70) cc_final: 0.7158 (t0) REVERT: I 80 TYR cc_start: 0.7664 (m-80) cc_final: 0.7027 (m-80) REVERT: I 104 MET cc_start: 0.8088 (mtm) cc_final: 0.7821 (mtt) REVERT: J 23 CYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8581 (t) REVERT: K 37 LEU cc_start: 0.7783 (mt) cc_final: 0.7561 (mt) REVERT: K 46 CYS cc_start: 0.8214 (m) cc_final: 0.7706 (m) REVERT: K 88 ASN cc_start: 0.7895 (m-40) cc_final: 0.7226 (p0) REVERT: K 90 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7596 (mm-30) REVERT: K 115 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.7189 (m-10) REVERT: K 140 SER cc_start: 0.8107 (p) cc_final: 0.7740 (m) REVERT: K 171 ASN cc_start: 0.6539 (m-40) cc_final: 0.6249 (p0) REVERT: K 219 LYS cc_start: 0.8174 (tttm) cc_final: 0.7615 (ttmm) REVERT: K 276 ASN cc_start: 0.7652 (t0) cc_final: 0.7382 (t0) REVERT: K 297 ASN cc_start: 0.6952 (m110) cc_final: 0.6727 (m-40) REVERT: K 383 ASN cc_start: 0.6753 (t0) cc_final: 0.6333 (t0) outliers start: 32 outliers final: 26 residues processed: 227 average time/residue: 0.2936 time to fit residues: 96.8243 Evaluate side-chains 243 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 212 time to evaluate : 1.746 ------------------------------------------------------------------------------- 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 23 CYS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain C residue 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 155 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 199 ASN 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 23 CYS Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 115 PHE 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 43 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 140 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.140851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.109401 restraints weight = 17803.880| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.18 r_work: 0.3015 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.464 14841 Z= 0.459 Angle : 0.709 45.770 20151 Z= 0.468 Chirality : 0.041 0.288 2241 Planarity : 0.006 0.256 2592 Dihedral : 4.629 29.302 2322 Min Nonbonded Distance : 0.625 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.97 % Allowed : 15.39 % Favored : 82.63 % Cbeta Deviations : 0.06 % 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: -1.37 (0.19), residues: 1788 helix: 0.35 (0.37), residues: 222 sheet: -0.60 (0.20), residues: 606 loop : -1.41 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 422 HIS 0.005 0.001 HIS E 141 PHE 0.028 0.001 PHE A 440 TYR 0.009 0.001 TYR C 60 ARG 0.008 0.000 ARG E 436 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3472.69 seconds wall clock time: 62 minutes 58.68 seconds (3778.68 seconds total)