Starting phenix.real_space_refine on Wed May 28 10:13:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vue_43529/05_2025/8vue_43529.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vue_43529/05_2025/8vue_43529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vue_43529/05_2025/8vue_43529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vue_43529/05_2025/8vue_43529.map" model { file = "/net/cci-nas-00/data/ceres_data/8vue_43529/05_2025/8vue_43529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vue_43529/05_2025/8vue_43529.cif" } resolution = 3.59 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= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11436 atoms to isotropic. 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 96 5.16 5 C 13512 2.51 5 N 3666 2.21 5 O 4227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21501 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2541 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 18, 'TRANS': 302} Chain: "B" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1328 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 1, 'TRANS': 162} Chain: "G" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1694 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1590 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 197} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: D, F, C, E, J, L, I, K Time building chain proxies: 10.40, per 1000 atoms: 0.48 Number of scatterers: 21501 At special positions: 0 Unit cell: (167.865, 185.193, 146.205, 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 96 16.00 O 4227 8.00 N 3666 7.00 C 13512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS B 471 " distance=2.08 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.02 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 482 " distance=2.03 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS D 471 " distance=1.99 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS F 471 " distance=2.02 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.03 Simple disulfide: pdb=" SG CYS E 59 " - pdb=" SG CYS E 71 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.03 Simple disulfide: pdb=" SG CYS E 282 " - pdb=" SG CYS E 306 " distance=2.02 Simple disulfide: pdb=" SG CYS D 478 " - pdb=" SG CYS D 482 " distance=2.03 Simple disulfide: pdb=" SG CYS F 478 " - pdb=" SG CYS F 482 " distance=2.03 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 NAG-ASN " NAG A 601 " - " ASN A 169 " " NAG C 601 " - " ASN C 169 " " NAG E 601 " - " ASN E 169 " Time building additional restraints: 5.56 Conformation dependent library (CDL) restraints added in 3.0 seconds 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5136 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 60 sheets defined 16.9% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 68 through 75 removed outlier: 3.807A pdb=" N ASP A 72 " --> pdb=" O PRO A 69 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLU A 73 " --> pdb=" O MET A 70 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 75 " --> pdb=" O ASP A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 110 Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.554A pdb=" N TRP A 126 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 371 through 393 removed outlier: 3.927A pdb=" N MET B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 460 Processing helix chain 'B' and resid 479 through 489 Processing helix chain 'C' and resid 60 through 67 Processing helix chain 'C' and resid 68 through 75 removed outlier: 3.807A pdb=" N ASP C 72 " --> pdb=" O PRO C 69 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLU C 73 " --> pdb=" O MET C 70 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE C 75 " --> pdb=" O ASP C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 110 Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.554A pdb=" N TRP C 126 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'D' and resid 371 through 393 removed outlier: 3.927A pdb=" N MET D 393 " --> pdb=" O ILE D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 460 Processing helix chain 'D' and resid 479 through 489 Processing helix chain 'E' and resid 60 through 67 Processing helix chain 'E' and resid 68 through 75 removed outlier: 3.808A pdb=" N ASP E 72 " --> pdb=" O PRO E 69 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N GLU E 73 " --> pdb=" O MET E 70 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE E 75 " --> pdb=" O ASP E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 110 Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.558A pdb=" N TRP E 126 " --> pdb=" O LYS E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 195 Processing helix chain 'F' and resid 371 through 393 removed outlier: 3.927A pdb=" N MET F 393 " --> pdb=" O ILE F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 460 Processing helix chain 'F' and resid 479 through 489 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.638A pdb=" N THR G 87 " --> pdb=" O PRO G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 158 No H-bonds generated for 'chain 'G' and resid 156 through 158' Processing helix chain 'G' and resid 185 through 190 removed outlier: 4.466A pdb=" N GLY G 190 " --> pdb=" O SER G 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 128 Processing helix chain 'H' and resid 183 through 188 Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.639A pdb=" N THR I 87 " --> pdb=" O PRO I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 158 No H-bonds generated for 'chain 'I' and resid 156 through 158' Processing helix chain 'I' and resid 185 through 190 removed outlier: 4.467A pdb=" N GLY I 190 " --> pdb=" O SER I 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.639A pdb=" N THR K 87 " --> pdb=" O PRO K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 156 through 158 No H-bonds generated for 'chain 'K' and resid 156 through 158' Processing helix chain 'K' and resid 185 through 190 removed outlier: 4.467A pdb=" N GLY K 190 " --> pdb=" O SER K 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 128 Processing helix chain 'J' and resid 183 through 188 Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'B' and resid 365 through 370 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA4, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.598A pdb=" N LEU A 54 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE A 83 " --> pdb=" O MET A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 97 through 99 removed outlier: 6.783A pdb=" N SER A 98 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N TRP A 234 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASP A 175 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS A 114 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS A 263 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE A 112 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 97 through 99 removed outlier: 6.783A pdb=" N SER A 98 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N TRP A 234 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.484A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 146 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB1, first strand: chain 'A' and resid 287 through 288 Processing sheet with id=AB2, first strand: chain 'D' and resid 365 through 370 Processing sheet with id=AB3, first strand: chain 'C' and resid 19 through 20 Processing sheet with id=AB4, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AB5, first strand: chain 'C' and resid 37 through 38 Processing sheet with id=AB6, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.599A pdb=" N LEU C 54 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE C 83 " --> pdb=" O MET C 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 97 through 99 removed outlier: 6.784A pdb=" N SER C 98 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N TRP C 234 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP C 175 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N HIS C 114 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LYS C 263 " --> pdb=" O ILE C 112 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE C 112 " --> pdb=" O LYS C 263 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 97 through 99 removed outlier: 6.784A pdb=" N SER C 98 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N TRP C 234 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.484A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER C 146 " --> pdb=" O CYS C 139 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC2, first strand: chain 'C' and resid 287 through 288 Processing sheet with id=AC3, first strand: chain 'F' and resid 365 through 370 Processing sheet with id=AC4, first strand: chain 'E' and resid 19 through 20 Processing sheet with id=AC5, first strand: chain 'E' and resid 33 through 35 Processing sheet with id=AC6, first strand: chain 'E' and resid 37 through 38 Processing sheet with id=AC7, first strand: chain 'E' and resid 54 through 55 removed outlier: 6.598A pdb=" N LEU E 54 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE E 83 " --> pdb=" O MET E 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 97 through 99 removed outlier: 6.783A pdb=" N SER E 98 " --> pdb=" O PHE E 232 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N TRP E 234 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASP E 175 " --> pdb=" O ILE E 260 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS E 114 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LYS E 263 " --> pdb=" O ILE E 112 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE E 112 " --> pdb=" O LYS E 263 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 97 through 99 removed outlier: 6.783A pdb=" N SER E 98 " --> pdb=" O PHE E 232 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N TRP E 234 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 136 through 141 removed outlier: 4.484A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER E 146 " --> pdb=" O CYS E 139 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD3, first strand: chain 'E' and resid 287 through 288 Processing sheet with id=AD4, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.517A pdb=" N VAL G 12 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP G 35A" --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG G 50 " --> pdb=" O TRP G 35A" (cutoff:3.500A) removed outlier: 6.441A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.517A pdb=" N VAL G 12 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N CYS G 92 " --> pdb=" O TRP G 103 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TRP G 103 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG G 94 " --> pdb=" O ASP G 101 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY G 96 " --> pdb=" O SER G 100F" (cutoff:3.500A) removed outlier: 8.081A pdb=" N SER G 100F" --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ARG G 98 " --> pdb=" O VAL G 100D" (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL G 100D" --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 120 through 124 removed outlier: 6.110A pdb=" N TYR G 176 " --> pdb=" O ASP G 144 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 120 through 124 removed outlier: 6.110A pdb=" N TYR G 176 " --> pdb=" O ASP G 144 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 151 through 154 Processing sheet with id=AE1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AE2, first strand: chain 'H' and resid 11 through 13 removed outlier: 3.581A pdb=" N GLU H 105 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 114 through 118 removed outlier: 5.256A pdb=" N SER H 131 " --> pdb=" O LEU H 181 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU H 181 " --> pdb=" O SER H 131 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL H 133 " --> pdb=" O LEU H 179 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU H 179 " --> pdb=" O VAL H 133 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU H 135 " --> pdb=" O SER H 177 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N SER H 177 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASN H 137 " --> pdb=" O LEU H 175 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU H 175 " --> pdb=" O ASN H 137 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 153 through 154 Processing sheet with id=AE5, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.517A pdb=" N VAL I 12 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP I 35A" --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG I 50 " --> pdb=" O TRP I 35A" (cutoff:3.500A) removed outlier: 6.440A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.517A pdb=" N VAL I 12 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS I 92 " --> pdb=" O TRP I 103 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TRP I 103 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG I 94 " --> pdb=" O ASP I 101 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY I 96 " --> pdb=" O SER I 100F" (cutoff:3.500A) removed outlier: 8.083A pdb=" N SER I 100F" --> pdb=" O GLY I 96 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ARG I 98 " --> pdb=" O VAL I 100D" (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL I 100D" --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 120 through 124 removed outlier: 6.108A pdb=" N TYR I 176 " --> pdb=" O ASP I 144 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 120 through 124 removed outlier: 6.108A pdb=" N TYR I 176 " --> pdb=" O ASP I 144 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 151 through 154 Processing sheet with id=AF2, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.517A pdb=" N VAL K 12 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TRP K 35A" --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG K 50 " --> pdb=" O TRP K 35A" (cutoff:3.500A) removed outlier: 6.443A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.517A pdb=" N VAL K 12 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS K 92 " --> pdb=" O TRP K 103 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TRP K 103 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG K 94 " --> pdb=" O ASP K 101 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY K 96 " --> pdb=" O SER K 100F" (cutoff:3.500A) removed outlier: 8.082A pdb=" N SER K 100F" --> pdb=" O GLY K 96 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ARG K 98 " --> pdb=" O VAL K 100D" (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL K 100D" --> pdb=" O ARG K 98 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 120 through 124 removed outlier: 6.110A pdb=" N TYR K 176 " --> pdb=" O ASP K 144 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 120 through 124 removed outlier: 6.110A pdb=" N TYR K 176 " --> pdb=" O ASP K 144 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 151 through 154 Processing sheet with id=AF8, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AF9, first strand: chain 'J' and resid 11 through 13 removed outlier: 3.583A pdb=" N GLU J 105 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 114 through 118 removed outlier: 5.255A pdb=" N SER J 131 " --> pdb=" O LEU J 181 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU J 181 " --> pdb=" O SER J 131 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL J 133 " --> pdb=" O LEU J 179 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU J 179 " --> pdb=" O VAL J 133 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU J 135 " --> pdb=" O SER J 177 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N SER J 177 " --> pdb=" O LEU J 135 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASN J 137 " --> pdb=" O LEU J 175 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU J 175 " --> pdb=" O ASN J 137 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 153 through 154 Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG4, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.581A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.254A pdb=" N SER L 131 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU L 181 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL L 133 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU L 179 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU L 135 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N SER L 177 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASN L 137 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU L 175 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 153 through 154 966 hydrogen bonds defined for protein. 2493 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: 9.12 Time building geometry restraints manager: 6.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 3597 1.29 - 1.43: 5799 1.43 - 1.56: 12465 1.56 - 1.70: 0 1.70 - 1.83: 129 Bond restraints: 21990 Sorted by residual: bond pdb=" CA SER G 100F" pdb=" CB SER G 100F" ideal model delta sigma weight residual 1.526 1.437 0.088 1.25e-02 6.40e+03 5.00e+01 bond pdb=" CA SER I 100F" pdb=" CB SER I 100F" ideal model delta sigma weight residual 1.526 1.438 0.088 1.25e-02 6.40e+03 4.94e+01 bond pdb=" CA SER K 100F" pdb=" CB SER K 100F" ideal model delta sigma weight residual 1.526 1.438 0.087 1.25e-02 6.40e+03 4.87e+01 bond pdb=" C VAL I 99 " pdb=" O VAL I 99 " ideal model delta sigma weight residual 1.236 1.154 0.082 1.19e-02 7.06e+03 4.81e+01 bond pdb=" C VAL K 99 " pdb=" O VAL K 99 " ideal model delta sigma weight residual 1.236 1.154 0.082 1.19e-02 7.06e+03 4.76e+01 ... (remaining 21985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 29077 2.54 - 5.08: 658 5.08 - 7.63: 99 7.63 - 10.17: 22 10.17 - 12.71: 6 Bond angle restraints: 29862 Sorted by residual: angle pdb=" CA THR L 29 " pdb=" CB THR L 29 " pdb=" OG1 THR L 29 " ideal model delta sigma weight residual 109.60 99.60 10.00 1.50e+00 4.44e-01 4.44e+01 angle pdb=" C SER J 31 " pdb=" N TYR J 32 " pdb=" CA TYR J 32 " ideal model delta sigma weight residual 121.54 134.25 -12.71 1.91e+00 2.74e-01 4.43e+01 angle pdb=" C SER L 31 " pdb=" N TYR L 32 " pdb=" CA TYR L 32 " ideal model delta sigma weight residual 121.54 134.25 -12.71 1.91e+00 2.74e-01 4.43e+01 angle pdb=" CA THR J 29 " pdb=" CB THR J 29 " pdb=" OG1 THR J 29 " ideal model delta sigma weight residual 109.60 99.63 9.97 1.50e+00 4.44e-01 4.42e+01 angle pdb=" C SER H 31 " pdb=" N TYR H 32 " pdb=" CA TYR H 32 " ideal model delta sigma weight residual 121.54 134.22 -12.68 1.91e+00 2.74e-01 4.40e+01 ... (remaining 29857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 11594 18.05 - 36.09: 1264 36.09 - 54.14: 270 54.14 - 72.19: 66 72.19 - 90.24: 24 Dihedral angle restraints: 13218 sinusoidal: 5226 harmonic: 7992 Sorted by residual: dihedral pdb=" CB CYS E 46 " pdb=" SG CYS E 46 " pdb=" SG CYS E 278 " pdb=" CB CYS E 278 " ideal model delta sinusoidal sigma weight residual -86.00 -15.13 -70.87 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CB CYS C 46 " pdb=" SG CYS C 46 " pdb=" SG CYS C 278 " pdb=" CB CYS C 278 " ideal model delta sinusoidal sigma weight residual -86.00 -15.15 -70.85 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CB CYS A 46 " pdb=" SG CYS A 46 " pdb=" SG CYS A 278 " pdb=" CB CYS A 278 " ideal model delta sinusoidal sigma weight residual -86.00 -15.15 -70.85 1 1.00e+01 1.00e-02 6.45e+01 ... (remaining 13215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 3062 0.091 - 0.182: 223 0.182 - 0.273: 13 0.273 - 0.364: 5 0.364 - 0.455: 9 Chirality restraints: 3312 Sorted by residual: chirality pdb=" CA VAL I 100D" pdb=" N VAL I 100D" pdb=" C VAL I 100D" pdb=" CB VAL I 100D" both_signs ideal model delta sigma weight residual False 2.44 2.90 -0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" CA VAL K 100D" pdb=" N VAL K 100D" pdb=" C VAL K 100D" pdb=" CB VAL K 100D" both_signs ideal model delta sigma weight residual False 2.44 2.90 -0.45 2.00e-01 2.50e+01 5.16e+00 chirality pdb=" CA VAL G 100D" pdb=" N VAL G 100D" pdb=" C VAL G 100D" pdb=" CB VAL G 100D" both_signs ideal model delta sigma weight residual False 2.44 2.89 -0.45 2.00e-01 2.50e+01 5.13e+00 ... (remaining 3309 not shown) Planarity restraints: 3858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA I 95 " -0.055 2.00e-02 2.50e+03 1.04e-01 1.09e+02 pdb=" C ALA I 95 " 0.180 2.00e-02 2.50e+03 pdb=" O ALA I 95 " -0.067 2.00e-02 2.50e+03 pdb=" N GLY I 96 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA K 95 " 0.054 2.00e-02 2.50e+03 1.04e-01 1.08e+02 pdb=" C ALA K 95 " -0.180 2.00e-02 2.50e+03 pdb=" O ALA K 95 " 0.067 2.00e-02 2.50e+03 pdb=" N GLY K 96 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 95 " -0.054 2.00e-02 2.50e+03 1.04e-01 1.08e+02 pdb=" C ALA G 95 " 0.180 2.00e-02 2.50e+03 pdb=" O ALA G 95 " -0.067 2.00e-02 2.50e+03 pdb=" N GLY G 96 " -0.058 2.00e-02 2.50e+03 ... (remaining 3855 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 115 2.44 - 3.06: 14206 3.06 - 3.67: 31723 3.67 - 4.29: 48475 4.29 - 4.90: 81854 Nonbonded interactions: 176373 Sorted by model distance: nonbonded pdb=" CB ALA K 93 " pdb=" CD1 LEU K 100G" model vdw 1.828 3.880 nonbonded pdb=" CB ALA G 93 " pdb=" CD1 LEU G 100G" model vdw 1.828 3.880 nonbonded pdb=" CB ALA I 93 " pdb=" CD1 LEU I 100G" model vdw 1.830 3.880 nonbonded pdb=" ND2 ASN I 100E" pdb=" O SER J 91 " model vdw 1.936 3.120 nonbonded pdb=" ND2 ASN K 100E" pdb=" O SER L 91 " model vdw 2.004 3.120 ... (remaining 176368 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: 0.13 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 50.290 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 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 0.088 22011 Z= 0.403 Angle : 0.949 12.709 29907 Z= 0.569 Chirality : 0.055 0.455 3312 Planarity : 0.006 0.104 3855 Dihedral : 15.990 90.236 8028 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.13 % Favored : 93.54 % Rotamer: Outliers : 4.98 % Allowed : 7.22 % Favored : 87.80 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.26 (0.14), residues: 2724 helix: -0.14 (0.24), residues: 384 sheet: -0.96 (0.16), residues: 849 loop : -2.26 (0.14), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 35A HIS 0.005 0.001 HIS E 12 PHE 0.017 0.002 PHE J 118 TYR 0.018 0.002 TYR B 358 ARG 0.004 0.001 ARG L 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 3) link_NAG-ASN : angle 3.17607 ( 9) hydrogen bonds : bond 0.13923 ( 879) hydrogen bonds : angle 7.24403 ( 2493) SS BOND : bond 0.01535 ( 18) SS BOND : angle 3.30269 ( 36) covalent geometry : bond 0.00724 (21990) covalent geometry : angle 0.94083 (29862) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 412 time to evaluate : 2.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.7154 (mtm) cc_final: 0.6860 (mtm) REVERT: A 293 MET cc_start: 0.8890 (mmt) cc_final: 0.8410 (mmt) REVERT: B 446 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7875 (t0) REVERT: D 395 THR cc_start: 0.7184 (t) cc_final: 0.6845 (p) REVERT: D 446 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7701 (t0) REVERT: E 293 MET cc_start: 0.8898 (mmt) cc_final: 0.8471 (mmt) REVERT: F 497 SER cc_start: 0.7624 (OUTLIER) cc_final: 0.7346 (t) REVERT: G 54 ARG cc_start: 0.7495 (ptt90) cc_final: 0.6847 (ptm-80) REVERT: G 209 LYS cc_start: 0.7865 (tppt) cc_final: 0.7492 (mmtp) REVERT: H 36 TYR cc_start: 0.8616 (m-80) cc_final: 0.8307 (m-10) REVERT: H 106 ILE cc_start: 0.7812 (mm) cc_final: 0.7336 (mm) REVERT: H 116 PHE cc_start: 0.7647 (m-80) cc_final: 0.7274 (m-10) REVERT: H 135 LEU cc_start: 0.9005 (mt) cc_final: 0.8689 (mp) REVERT: H 171 SER cc_start: 0.8817 (OUTLIER) cc_final: 0.8552 (p) REVERT: H 188 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8245 (mttm) REVERT: H 189 HIS cc_start: 0.8646 (m90) cc_final: 0.8133 (m-70) REVERT: I 154 TRP cc_start: 0.7978 (m100) cc_final: 0.6276 (m100) REVERT: I 179 SER cc_start: 0.7097 (OUTLIER) cc_final: 0.6835 (p) REVERT: I 209 LYS cc_start: 0.8310 (tppt) cc_final: 0.7863 (mmtp) REVERT: K 122 PHE cc_start: 0.7540 (m-10) cc_final: 0.6975 (m-10) REVERT: K 154 TRP cc_start: 0.7956 (m100) cc_final: 0.7524 (m100) REVERT: K 176 TYR cc_start: 0.8797 (m-10) cc_final: 0.8266 (m-80) REVERT: K 179 SER cc_start: 0.6844 (OUTLIER) cc_final: 0.6635 (p) REVERT: K 209 LYS cc_start: 0.8564 (tppt) cc_final: 0.8273 (mmtp) REVERT: J 70 ASP cc_start: 0.7056 (m-30) cc_final: 0.6541 (m-30) REVERT: J 106 ILE cc_start: 0.7657 (mm) cc_final: 0.7088 (mm) REVERT: J 189 HIS cc_start: 0.8513 (m90) cc_final: 0.8188 (m90) REVERT: J 190 LYS cc_start: 0.8041 (tptt) cc_final: 0.7405 (tppt) REVERT: J 210 ASN cc_start: 0.8568 (m-40) cc_final: 0.8207 (t0) REVERT: L 106 ILE cc_start: 0.7788 (mm) cc_final: 0.7312 (mm) REVERT: L 190 LYS cc_start: 0.8194 (tptt) cc_final: 0.7751 (tppt) outliers start: 120 outliers final: 27 residues processed: 499 average time/residue: 0.3821 time to fit residues: 278.1262 Evaluate side-chains 261 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 227 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 446 ASP Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain F residue 366 SER Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 458 LEU Chi-restraints excluded: chain F residue 497 SER Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 148 GLU Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 188 LYS Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 100 ASN Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 171 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 20.0000 chunk 204 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 211 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 128 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 245 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 ASN A 119 GLN A 183 HIS C 4 GLN ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 119 GLN ** D 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 ASN E 119 GLN G 6 GLN G 155 ASN G 192 GLN G 197 ASN G 204 ASN H 27 GLN H 55 GLN H 124 GLN ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 192 GLN I 197 ASN I 204 ASN K 6 GLN K 155 ASN K 204 ASN J 27 GLN J 38 GLN J 55 GLN J 124 GLN ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 158 ASN J 199 GLN L 27 GLN L 38 GLN L 55 GLN L 147 GLN L 158 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.108260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.079430 restraints weight = 51319.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.082068 restraints weight = 23851.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.083729 restraints weight = 14758.303| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22011 Z= 0.150 Angle : 0.641 7.592 29907 Z= 0.341 Chirality : 0.045 0.156 3312 Planarity : 0.005 0.076 3855 Dihedral : 6.153 45.024 3063 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.62 % Allowed : 11.75 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % 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: -0.97 (0.16), residues: 2724 helix: 1.28 (0.25), residues: 402 sheet: -0.24 (0.17), residues: 870 loop : -1.49 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 148 HIS 0.010 0.001 HIS L 198 PHE 0.026 0.002 PHE I 122 TYR 0.028 0.001 TYR J 140 ARG 0.006 0.001 ARG G 43 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 3) link_NAG-ASN : angle 1.99305 ( 9) hydrogen bonds : bond 0.04366 ( 879) hydrogen bonds : angle 5.46689 ( 2493) SS BOND : bond 0.00268 ( 18) SS BOND : angle 1.85239 ( 36) covalent geometry : bond 0.00330 (21990) covalent geometry : angle 0.63691 (29862) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 280 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8220 (t0) REVERT: A 293 MET cc_start: 0.9092 (mmt) cc_final: 0.8496 (mmt) REVERT: B 436 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.8031 (mtm) REVERT: B 437 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8059 (mm-30) REVERT: C 305 GLU cc_start: 0.7881 (mp0) cc_final: 0.7381 (pp20) REVERT: D 437 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8074 (mm-30) REVERT: E 241 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8181 (t0) REVERT: E 286 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7816 (ptp) REVERT: E 293 MET cc_start: 0.9128 (mmt) cc_final: 0.8609 (mmt) REVERT: F 437 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7900 (mm-30) REVERT: G 144 ASP cc_start: 0.7024 (t0) cc_final: 0.6721 (t0) REVERT: G 154 TRP cc_start: 0.7917 (m100) cc_final: 0.7193 (m100) REVERT: G 196 CYS cc_start: 0.7486 (OUTLIER) cc_final: 0.6389 (p) REVERT: G 209 LYS cc_start: 0.8043 (tppt) cc_final: 0.7554 (mmtp) REVERT: H 24 ARG cc_start: 0.8282 (ttm110) cc_final: 0.8076 (ttm110) REVERT: H 30 SER cc_start: 0.9199 (t) cc_final: 0.8965 (p) REVERT: H 36 TYR cc_start: 0.8824 (m-80) cc_final: 0.8458 (m-10) REVERT: H 116 PHE cc_start: 0.7338 (m-80) cc_final: 0.7132 (m-80) REVERT: H 118 PHE cc_start: 0.7531 (m-80) cc_final: 0.6972 (m-80) REVERT: H 138 ASN cc_start: 0.8270 (m-40) cc_final: 0.7675 (t0) REVERT: H 190 LYS cc_start: 0.8109 (tptt) cc_final: 0.7600 (tppt) REVERT: I 85 GLU cc_start: 0.8276 (mp0) cc_final: 0.7987 (mp0) REVERT: I 154 TRP cc_start: 0.7719 (m100) cc_final: 0.6834 (m100) REVERT: I 209 LYS cc_start: 0.8100 (tppt) cc_final: 0.7792 (mmtm) REVERT: K 144 ASP cc_start: 0.7157 (t0) cc_final: 0.6888 (t0) REVERT: K 166 PHE cc_start: 0.7683 (m-10) cc_final: 0.7328 (m-10) REVERT: K 179 SER cc_start: 0.7011 (OUTLIER) cc_final: 0.6581 (p) REVERT: J 24 ARG cc_start: 0.8135 (ttm110) cc_final: 0.7378 (ttm110) REVERT: J 118 PHE cc_start: 0.7091 (m-10) cc_final: 0.6740 (m-10) REVERT: J 142 ARG cc_start: 0.8619 (tpp80) cc_final: 0.8108 (mmm-85) REVERT: J 189 HIS cc_start: 0.8265 (m90) cc_final: 0.7990 (m90) REVERT: J 190 LYS cc_start: 0.8198 (tptt) cc_final: 0.7555 (tppt) REVERT: L 24 ARG cc_start: 0.8366 (ttm110) cc_final: 0.7960 (ttm-80) REVERT: L 30 SER cc_start: 0.9238 (t) cc_final: 0.8970 (p) REVERT: L 36 TYR cc_start: 0.8928 (m-80) cc_final: 0.8713 (m-10) REVERT: L 61 ARG cc_start: 0.8586 (mtm-85) cc_final: 0.8285 (mtm-85) REVERT: L 142 ARG cc_start: 0.8641 (tpp80) cc_final: 0.8100 (mmm160) REVERT: L 190 LYS cc_start: 0.8159 (tptt) cc_final: 0.7831 (tppt) outliers start: 63 outliers final: 26 residues processed: 328 average time/residue: 0.3354 time to fit residues: 166.9431 Evaluate side-chains 254 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 222 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 115 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 97 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 72 optimal weight: 0.0970 chunk 138 optimal weight: 0.9980 chunk 232 optimal weight: 2.9990 chunk 217 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 105 optimal weight: 0.0070 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 ASN ** D 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 359 HIS ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 GLN G 100EASN G 197 ASN H 38 GLN H 124 GLN H 147 GLN I 197 ASN K 6 GLN K 192 GLN K 197 ASN ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.106849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.078080 restraints weight = 51465.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.080612 restraints weight = 23898.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.082241 restraints weight = 14901.141| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22011 Z= 0.151 Angle : 0.601 8.438 29907 Z= 0.317 Chirality : 0.044 0.166 3312 Planarity : 0.005 0.070 3855 Dihedral : 5.104 38.871 3012 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.37 % Allowed : 14.45 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % 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: -0.48 (0.16), residues: 2724 helix: 1.66 (0.25), residues: 405 sheet: 0.16 (0.18), residues: 864 loop : -1.21 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 148 HIS 0.007 0.001 HIS A 32 PHE 0.020 0.002 PHE H 139 TYR 0.016 0.001 TYR J 140 ARG 0.004 0.000 ARG A 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 3) link_NAG-ASN : angle 2.08913 ( 9) hydrogen bonds : bond 0.04147 ( 879) hydrogen bonds : angle 5.07242 ( 2493) SS BOND : bond 0.00418 ( 18) SS BOND : angle 1.72412 ( 36) covalent geometry : bond 0.00343 (21990) covalent geometry : angle 0.59777 (29862) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 247 time to evaluate : 2.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.9117 (mmt) cc_final: 0.8520 (mmt) REVERT: C 305 GLU cc_start: 0.7824 (mp0) cc_final: 0.7392 (pp20) REVERT: D 437 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7974 (mm-30) REVERT: E 241 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.8134 (t0) REVERT: E 293 MET cc_start: 0.9148 (mmt) cc_final: 0.8663 (mmt) REVERT: G 144 ASP cc_start: 0.6946 (t0) cc_final: 0.6672 (t0) REVERT: G 154 TRP cc_start: 0.7992 (m100) cc_final: 0.7761 (m100) REVERT: G 176 TYR cc_start: 0.8125 (m-80) cc_final: 0.7900 (m-80) REVERT: G 196 CYS cc_start: 0.7413 (OUTLIER) cc_final: 0.6645 (p) REVERT: G 209 LYS cc_start: 0.8108 (tppt) cc_final: 0.7631 (mmtp) REVERT: H 36 TYR cc_start: 0.8923 (m-80) cc_final: 0.8676 (m-10) REVERT: H 116 PHE cc_start: 0.7412 (m-80) cc_final: 0.7191 (m-80) REVERT: H 118 PHE cc_start: 0.7466 (m-80) cc_final: 0.6854 (m-10) REVERT: H 138 ASN cc_start: 0.8023 (m-40) cc_final: 0.7549 (t0) REVERT: H 187 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8373 (mp0) REVERT: H 189 HIS cc_start: 0.8028 (m-70) cc_final: 0.7621 (m-70) REVERT: H 190 LYS cc_start: 0.8042 (tptt) cc_final: 0.7770 (tppt) REVERT: H 192 TYR cc_start: 0.8511 (m-10) cc_final: 0.8054 (m-10) REVERT: I 13 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7815 (mtmm) REVERT: I 154 TRP cc_start: 0.7776 (m100) cc_final: 0.6498 (m100) REVERT: I 209 LYS cc_start: 0.7786 (tppt) cc_final: 0.7553 (mmtp) REVERT: K 105 GLN cc_start: 0.8746 (pp30) cc_final: 0.7901 (pp30) REVERT: K 144 ASP cc_start: 0.7151 (t0) cc_final: 0.6882 (t0) REVERT: K 154 TRP cc_start: 0.8066 (m100) cc_final: 0.7647 (m100) REVERT: K 166 PHE cc_start: 0.7920 (m-80) cc_final: 0.7596 (m-10) REVERT: J 70 ASP cc_start: 0.7700 (m-30) cc_final: 0.7488 (m-30) REVERT: J 118 PHE cc_start: 0.7048 (m-80) cc_final: 0.6829 (m-10) REVERT: J 142 ARG cc_start: 0.8556 (tpp80) cc_final: 0.8045 (mmm-85) REVERT: J 143 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7456 (pm20) REVERT: J 190 LYS cc_start: 0.7928 (tptt) cc_final: 0.7541 (tppt) REVERT: L 24 ARG cc_start: 0.8479 (ttm110) cc_final: 0.8254 (ttm-80) REVERT: L 30 SER cc_start: 0.9265 (t) cc_final: 0.8930 (p) REVERT: L 36 TYR cc_start: 0.8894 (m-80) cc_final: 0.8676 (m-10) REVERT: L 108 ARG cc_start: 0.8189 (ptm160) cc_final: 0.7928 (ptm160) REVERT: L 192 TYR cc_start: 0.6889 (m-10) cc_final: 0.6672 (m-10) outliers start: 57 outliers final: 36 residues processed: 290 average time/residue: 0.3681 time to fit residues: 163.2559 Evaluate side-chains 258 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 218 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 201 LYS Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 209 PHE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 197 ASN Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 201 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 116 optimal weight: 0.0000 chunk 122 optimal weight: 0.9980 chunk 263 optimal weight: 8.9990 chunk 220 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 192 optimal weight: 0.4980 chunk 223 optimal weight: 0.7980 chunk 172 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 ASN ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 GLN I 197 ASN K 197 ASN J 147 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.101883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.073026 restraints weight = 52181.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.075582 restraints weight = 23802.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.077223 restraints weight = 14695.999| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22011 Z= 0.133 Angle : 0.570 8.103 29907 Z= 0.299 Chirality : 0.043 0.158 3312 Planarity : 0.004 0.069 3855 Dihedral : 4.847 38.547 3009 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.53 % Allowed : 15.77 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % 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: -0.19 (0.16), residues: 2724 helix: 1.92 (0.25), residues: 408 sheet: 0.35 (0.18), residues: 864 loop : -1.05 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 148 HIS 0.006 0.001 HIS A 32 PHE 0.018 0.001 PHE L 139 TYR 0.027 0.001 TYR H 173 ARG 0.005 0.000 ARG H 142 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 3) link_NAG-ASN : angle 2.07405 ( 9) hydrogen bonds : bond 0.03906 ( 879) hydrogen bonds : angle 4.84461 ( 2493) SS BOND : bond 0.00308 ( 18) SS BOND : angle 1.50812 ( 36) covalent geometry : bond 0.00300 (21990) covalent geometry : angle 0.56696 (29862) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 250 time to evaluate : 2.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ARG cc_start: 0.8621 (mmm-85) cc_final: 0.8371 (mmm-85) REVERT: A 230 MET cc_start: 0.8148 (mtm) cc_final: 0.7918 (mtp) REVERT: A 293 MET cc_start: 0.9104 (mmt) cc_final: 0.8458 (mmt) REVERT: E 241 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8078 (t0) REVERT: E 293 MET cc_start: 0.9197 (mmt) cc_final: 0.8708 (mmt) REVERT: F 424 ASP cc_start: 0.7760 (t0) cc_final: 0.7556 (t0) REVERT: G 105 GLN cc_start: 0.8676 (pp30) cc_final: 0.8356 (pp30) REVERT: G 144 ASP cc_start: 0.7039 (t0) cc_final: 0.6666 (t0) REVERT: G 171 GLN cc_start: 0.7985 (tm130) cc_final: 0.7211 (mt0) REVERT: G 192 GLN cc_start: 0.5285 (OUTLIER) cc_final: 0.4844 (mm110) REVERT: G 196 CYS cc_start: 0.7433 (t) cc_final: 0.6337 (p) REVERT: G 209 LYS cc_start: 0.7972 (tppt) cc_final: 0.7526 (mmtp) REVERT: H 24 ARG cc_start: 0.8463 (ttm110) cc_final: 0.8004 (ttm110) REVERT: H 116 PHE cc_start: 0.7520 (m-80) cc_final: 0.7300 (m-80) REVERT: H 118 PHE cc_start: 0.7371 (m-80) cc_final: 0.7002 (m-10) REVERT: H 167 ASP cc_start: 0.8150 (t70) cc_final: 0.7865 (t0) REVERT: H 187 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8317 (mm-30) REVERT: H 189 HIS cc_start: 0.7972 (m-70) cc_final: 0.7675 (m-70) REVERT: H 190 LYS cc_start: 0.8049 (tptt) cc_final: 0.7628 (tppt) REVERT: I 13 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7889 (mtmm) REVERT: I 105 GLN cc_start: 0.8704 (pp30) cc_final: 0.7869 (pp30) REVERT: I 154 TRP cc_start: 0.7784 (m100) cc_final: 0.6747 (m100) REVERT: I 176 TYR cc_start: 0.8237 (m-80) cc_final: 0.7969 (m-80) REVERT: K 32 ASP cc_start: 0.8875 (p0) cc_final: 0.8522 (p0) REVERT: K 105 GLN cc_start: 0.8721 (pp30) cc_final: 0.7864 (pp30) REVERT: K 144 ASP cc_start: 0.7231 (t0) cc_final: 0.7026 (t0) REVERT: K 166 PHE cc_start: 0.8055 (m-80) cc_final: 0.7730 (m-10) REVERT: K 192 GLN cc_start: 0.4367 (OUTLIER) cc_final: 0.3402 (mm110) REVERT: J 116 PHE cc_start: 0.8014 (m-10) cc_final: 0.7744 (m-10) REVERT: J 142 ARG cc_start: 0.8608 (tpp80) cc_final: 0.7777 (mmm-85) REVERT: J 143 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7388 (pm20) REVERT: J 190 LYS cc_start: 0.7855 (tptt) cc_final: 0.7537 (tppt) REVERT: L 30 SER cc_start: 0.9173 (t) cc_final: 0.8780 (p) REVERT: L 36 TYR cc_start: 0.8859 (m-80) cc_final: 0.8575 (m-10) REVERT: L 192 TYR cc_start: 0.7034 (m-10) cc_final: 0.6737 (m-10) REVERT: L 195 GLU cc_start: 0.6490 (tm-30) cc_final: 0.6241 (tp30) outliers start: 61 outliers final: 39 residues processed: 298 average time/residue: 0.3521 time to fit residues: 158.6052 Evaluate side-chains 266 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 222 time to evaluate : 2.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 278 CYS Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 192 GLN Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 209 PHE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 192 GLN Chi-restraints excluded: chain K residue 196 CYS Chi-restraints excluded: chain K residue 198 VAL Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 201 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 208 optimal weight: 0.3980 chunk 128 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 101 optimal weight: 0.9980 chunk 249 optimal weight: 0.6980 chunk 218 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 260 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 HIS ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 HIS ** D 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 ASN K 197 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.100410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.072299 restraints weight = 51417.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.074743 restraints weight = 23508.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.076317 restraints weight = 14564.676| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22011 Z= 0.149 Angle : 0.573 8.117 29907 Z= 0.300 Chirality : 0.043 0.153 3312 Planarity : 0.004 0.066 3855 Dihedral : 4.791 38.253 3009 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.82 % Allowed : 16.40 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % 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: -0.07 (0.16), residues: 2724 helix: 2.04 (0.25), residues: 408 sheet: 0.41 (0.18), residues: 873 loop : -0.97 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 148 HIS 0.007 0.001 HIS J 198 PHE 0.019 0.002 PHE L 139 TYR 0.020 0.001 TYR H 173 ARG 0.005 0.000 ARG J 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00229 ( 3) link_NAG-ASN : angle 2.12779 ( 9) hydrogen bonds : bond 0.03924 ( 879) hydrogen bonds : angle 4.77744 ( 2493) SS BOND : bond 0.00405 ( 18) SS BOND : angle 1.57177 ( 36) covalent geometry : bond 0.00341 (21990) covalent geometry : angle 0.57006 (29862) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 237 time to evaluate : 2.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LYS cc_start: 0.9013 (mttp) cc_final: 0.8759 (mtmm) REVERT: A 293 MET cc_start: 0.9096 (mmt) cc_final: 0.8451 (mmt) REVERT: B 477 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8499 (tppt) REVERT: C 269 MET cc_start: 0.8149 (ttm) cc_final: 0.7706 (mtp) REVERT: E 57 ARG cc_start: 0.7871 (ttm110) cc_final: 0.7600 (ttm110) REVERT: E 241 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8101 (t0) REVERT: E 293 MET cc_start: 0.9134 (mmt) cc_final: 0.8640 (mmt) REVERT: G 105 GLN cc_start: 0.8667 (pp30) cc_final: 0.8352 (pp30) REVERT: G 144 ASP cc_start: 0.6959 (t0) cc_final: 0.6713 (t0) REVERT: G 154 TRP cc_start: 0.8042 (m100) cc_final: 0.7273 (m100) REVERT: G 192 GLN cc_start: 0.5723 (OUTLIER) cc_final: 0.5453 (mm110) REVERT: G 196 CYS cc_start: 0.7542 (t) cc_final: 0.6465 (p) REVERT: G 209 LYS cc_start: 0.7889 (tppt) cc_final: 0.7461 (mmtp) REVERT: H 24 ARG cc_start: 0.8445 (ttm110) cc_final: 0.8181 (ttm110) REVERT: H 167 ASP cc_start: 0.8175 (t70) cc_final: 0.7860 (t0) REVERT: H 189 HIS cc_start: 0.7722 (m-70) cc_final: 0.7381 (m-70) REVERT: H 190 LYS cc_start: 0.8029 (tptt) cc_final: 0.7722 (tppt) REVERT: H 192 TYR cc_start: 0.8175 (m-10) cc_final: 0.7682 (m-10) REVERT: I 13 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7911 (mtmm) REVERT: I 105 GLN cc_start: 0.8673 (pp30) cc_final: 0.7888 (pp30) REVERT: K 3 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7525 (mp10) REVERT: K 32 ASP cc_start: 0.8922 (p0) cc_final: 0.8616 (p0) REVERT: K 46 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8129 (mt-10) REVERT: K 105 GLN cc_start: 0.8710 (pp30) cc_final: 0.7887 (pp30) REVERT: K 117 LYS cc_start: 0.8321 (mmtm) cc_final: 0.8102 (mmtt) REVERT: K 166 PHE cc_start: 0.7924 (m-80) cc_final: 0.7560 (m-10) REVERT: J 142 ARG cc_start: 0.8582 (tpp80) cc_final: 0.7730 (mmm-85) REVERT: J 143 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7457 (pm20) REVERT: J 190 LYS cc_start: 0.7857 (tptt) cc_final: 0.7555 (tppt) REVERT: L 30 SER cc_start: 0.9097 (t) cc_final: 0.8685 (p) REVERT: L 36 TYR cc_start: 0.8892 (m-80) cc_final: 0.8546 (m-10) REVERT: L 192 TYR cc_start: 0.7408 (m-10) cc_final: 0.7161 (m-10) REVERT: L 195 GLU cc_start: 0.6394 (tm-30) cc_final: 0.5988 (tp30) outliers start: 68 outliers final: 47 residues processed: 293 average time/residue: 0.3519 time to fit residues: 156.1538 Evaluate side-chains 271 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 218 time to evaluate : 2.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 477 LYS Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 278 CYS Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 192 GLN Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 209 PHE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 197 ASN Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 201 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 142 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 237 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 GLN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100EASN I 197 ASN K 197 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.105563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.076751 restraints weight = 52392.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.079214 restraints weight = 24181.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.080776 restraints weight = 15037.498| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 22011 Z= 0.215 Angle : 0.625 8.613 29907 Z= 0.327 Chirality : 0.045 0.167 3312 Planarity : 0.004 0.068 3855 Dihedral : 5.030 39.393 3009 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.20 % Allowed : 16.31 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % 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: -0.14 (0.16), residues: 2724 helix: 1.89 (0.24), residues: 408 sheet: 0.40 (0.18), residues: 864 loop : -1.00 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 148 HIS 0.009 0.001 HIS J 198 PHE 0.021 0.002 PHE H 118 TYR 0.018 0.001 TYR H 173 ARG 0.006 0.000 ARG J 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 3) link_NAG-ASN : angle 2.29425 ( 9) hydrogen bonds : bond 0.04279 ( 879) hydrogen bonds : angle 4.93449 ( 2493) SS BOND : bond 0.00445 ( 18) SS BOND : angle 1.89458 ( 36) covalent geometry : bond 0.00496 (21990) covalent geometry : angle 0.62060 (29862) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 227 time to evaluate : 2.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8277 (ttm110) cc_final: 0.7847 (ttm110) REVERT: A 293 MET cc_start: 0.9065 (mmt) cc_final: 0.8470 (mmt) REVERT: C 28 VAL cc_start: 0.9053 (OUTLIER) cc_final: 0.8837 (p) REVERT: C 269 MET cc_start: 0.8163 (ttm) cc_final: 0.7742 (mtp) REVERT: E 57 ARG cc_start: 0.7883 (ttm110) cc_final: 0.7537 (ttm110) REVERT: E 241 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.8070 (t0) REVERT: E 293 MET cc_start: 0.9114 (mmt) cc_final: 0.8667 (mmt) REVERT: F 377 LYS cc_start: 0.8705 (ttmt) cc_final: 0.8116 (ttmm) REVERT: F 439 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7360 (tm-30) REVERT: G 105 GLN cc_start: 0.8778 (pp30) cc_final: 0.7951 (pp30) REVERT: G 145 TYR cc_start: 0.6602 (p90) cc_final: 0.6345 (p90) REVERT: G 196 CYS cc_start: 0.7544 (t) cc_final: 0.6442 (p) REVERT: G 209 LYS cc_start: 0.8004 (tppt) cc_final: 0.7474 (mmtp) REVERT: H 24 ARG cc_start: 0.8411 (ttm110) cc_final: 0.8157 (ttm110) REVERT: H 138 ASN cc_start: 0.7991 (m110) cc_final: 0.7287 (m-40) REVERT: H 161 GLU cc_start: 0.8960 (pp20) cc_final: 0.8566 (pp20) REVERT: H 167 ASP cc_start: 0.8308 (t70) cc_final: 0.7921 (t0) REVERT: H 189 HIS cc_start: 0.7737 (m-70) cc_final: 0.7417 (m-70) REVERT: I 13 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7969 (mtmm) REVERT: I 46 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7885 (mt-10) REVERT: I 105 GLN cc_start: 0.8818 (pp30) cc_final: 0.8019 (pp30) REVERT: I 122 PHE cc_start: 0.8060 (m-80) cc_final: 0.7732 (m-80) REVERT: I 154 TRP cc_start: 0.7775 (m100) cc_final: 0.7543 (m100) REVERT: K 32 ASP cc_start: 0.8975 (p0) cc_final: 0.8688 (p0) REVERT: K 105 GLN cc_start: 0.8766 (pp30) cc_final: 0.7971 (pp30) REVERT: J 105 GLU cc_start: 0.8059 (tp30) cc_final: 0.7295 (tp30) REVERT: J 138 ASN cc_start: 0.8119 (m110) cc_final: 0.7672 (p0) REVERT: J 143 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7364 (pm20) REVERT: J 187 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8289 (mm-30) REVERT: J 190 LYS cc_start: 0.8172 (tptt) cc_final: 0.7863 (tppt) REVERT: L 30 SER cc_start: 0.9080 (t) cc_final: 0.8673 (p) REVERT: L 36 TYR cc_start: 0.8956 (m-80) cc_final: 0.8587 (m-10) REVERT: L 167 ASP cc_start: 0.8424 (t70) cc_final: 0.8164 (t0) REVERT: L 195 GLU cc_start: 0.6129 (tm-30) cc_final: 0.5764 (tp30) outliers start: 77 outliers final: 55 residues processed: 296 average time/residue: 0.3377 time to fit residues: 152.7253 Evaluate side-chains 267 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 208 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 477 LYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 478 CYS Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 278 CYS Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 482 CYS Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 209 PHE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain I residue 210 LYS Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 198 VAL Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 201 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 214 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 128 optimal weight: 0.2980 chunk 216 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 HIS ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100EASN I 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.101244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.072864 restraints weight = 51444.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.075317 restraints weight = 23908.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.076899 restraints weight = 14900.197| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22011 Z= 0.127 Angle : 0.576 8.634 29907 Z= 0.301 Chirality : 0.044 0.156 3312 Planarity : 0.004 0.068 3855 Dihedral : 4.769 38.432 3009 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.41 % Allowed : 17.35 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % 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: 0.02 (0.16), residues: 2724 helix: 2.08 (0.25), residues: 408 sheet: 0.43 (0.18), residues: 870 loop : -0.86 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 148 HIS 0.010 0.001 HIS J 198 PHE 0.020 0.001 PHE L 139 TYR 0.015 0.001 TYR H 173 ARG 0.008 0.000 ARG J 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 3) link_NAG-ASN : angle 2.21408 ( 9) hydrogen bonds : bond 0.03771 ( 879) hydrogen bonds : angle 4.74129 ( 2493) SS BOND : bond 0.00279 ( 18) SS BOND : angle 1.44314 ( 36) covalent geometry : bond 0.00287 (21990) covalent geometry : angle 0.57247 (29862) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 242 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8280 (ttm110) cc_final: 0.8014 (ttm110) REVERT: B 451 ASN cc_start: 0.8226 (m-40) cc_final: 0.7911 (t0) REVERT: B 477 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8496 (tppt) REVERT: C 57 ARG cc_start: 0.7837 (ttm110) cc_final: 0.7512 (ttm110) REVERT: C 269 MET cc_start: 0.8057 (ttm) cc_final: 0.7647 (mtp) REVERT: E 57 ARG cc_start: 0.7839 (ttm110) cc_final: 0.7575 (ttm110) REVERT: E 241 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8110 (t0) REVERT: E 293 MET cc_start: 0.9134 (mmt) cc_final: 0.8660 (mmt) REVERT: F 439 GLU cc_start: 0.7524 (tm-30) cc_final: 0.7264 (tm-30) REVERT: G 105 GLN cc_start: 0.8632 (pp30) cc_final: 0.7796 (pp30) REVERT: G 154 TRP cc_start: 0.8126 (m100) cc_final: 0.7541 (m100) REVERT: G 196 CYS cc_start: 0.7314 (t) cc_final: 0.6202 (p) REVERT: H 24 ARG cc_start: 0.8489 (ttm110) cc_final: 0.8212 (ttm110) REVERT: H 138 ASN cc_start: 0.7974 (m110) cc_final: 0.7284 (m-40) REVERT: H 161 GLU cc_start: 0.8958 (pp20) cc_final: 0.8526 (pp20) REVERT: H 167 ASP cc_start: 0.8252 (t70) cc_final: 0.7886 (t0) REVERT: H 189 HIS cc_start: 0.7699 (m-70) cc_final: 0.7306 (m-70) REVERT: I 13 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7903 (mtmm) REVERT: I 46 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8019 (mt-10) REVERT: I 105 GLN cc_start: 0.8701 (pp30) cc_final: 0.7896 (pp30) REVERT: I 117 LYS cc_start: 0.8217 (mptt) cc_final: 0.7951 (mmtt) REVERT: K 32 ASP cc_start: 0.8946 (p0) cc_final: 0.8634 (p0) REVERT: K 100 ASN cc_start: 0.8450 (m-40) cc_final: 0.8110 (m-40) REVERT: K 105 GLN cc_start: 0.8651 (pp30) cc_final: 0.7855 (pp30) REVERT: K 117 LYS cc_start: 0.8299 (mmtm) cc_final: 0.8026 (mptt) REVERT: K 154 TRP cc_start: 0.8190 (m100) cc_final: 0.7982 (m100) REVERT: K 166 PHE cc_start: 0.7885 (m-10) cc_final: 0.7681 (m-10) REVERT: J 105 GLU cc_start: 0.7953 (tp30) cc_final: 0.7237 (tp30) REVERT: J 143 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7292 (pm20) REVERT: J 161 GLU cc_start: 0.8965 (pp20) cc_final: 0.8437 (pp20) REVERT: J 167 ASP cc_start: 0.8328 (t70) cc_final: 0.8060 (t0) REVERT: J 187 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8282 (mm-30) REVERT: J 190 LYS cc_start: 0.8188 (tptt) cc_final: 0.7892 (tppt) REVERT: L 24 ARG cc_start: 0.8255 (ttm110) cc_final: 0.8051 (ttm110) REVERT: L 36 TYR cc_start: 0.8913 (m-80) cc_final: 0.8562 (m-10) REVERT: L 138 ASN cc_start: 0.7990 (m110) cc_final: 0.7228 (m-40) REVERT: L 167 ASP cc_start: 0.8382 (t70) cc_final: 0.8152 (t0) REVERT: L 170 ASP cc_start: 0.6998 (t0) cc_final: 0.6650 (t0) REVERT: L 181 LEU cc_start: 0.7192 (pt) cc_final: 0.6209 (pt) REVERT: L 195 GLU cc_start: 0.6347 (tm-30) cc_final: 0.5955 (tp30) outliers start: 58 outliers final: 42 residues processed: 294 average time/residue: 0.3549 time to fit residues: 158.0708 Evaluate side-chains 268 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 222 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 477 LYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 478 CYS Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 278 CYS Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 482 CYS Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 209 PHE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 197 ASN Chi-restraints excluded: chain K residue 198 VAL Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 201 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 237 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 224 optimal weight: 8.9990 chunk 200 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 ASN ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 476 HIS ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.102160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.073541 restraints weight = 52034.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.075978 restraints weight = 24143.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.077542 restraints weight = 15020.143| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22011 Z= 0.221 Angle : 0.642 10.158 29907 Z= 0.334 Chirality : 0.045 0.147 3312 Planarity : 0.004 0.064 3855 Dihedral : 5.028 39.386 3009 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.70 % Allowed : 17.60 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % 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: -0.04 (0.16), residues: 2724 helix: 2.01 (0.25), residues: 402 sheet: 0.37 (0.18), residues: 894 loop : -0.89 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 426 HIS 0.010 0.001 HIS J 198 PHE 0.023 0.002 PHE J 118 TYR 0.018 0.001 TYR F 496 ARG 0.008 0.000 ARG J 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 3) link_NAG-ASN : angle 2.38541 ( 9) hydrogen bonds : bond 0.04246 ( 879) hydrogen bonds : angle 4.97470 ( 2493) SS BOND : bond 0.00413 ( 18) SS BOND : angle 1.93604 ( 36) covalent geometry : bond 0.00512 (21990) covalent geometry : angle 0.63765 (29862) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 220 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8330 (ttm110) cc_final: 0.7827 (ttm110) REVERT: B 477 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8527 (tppt) REVERT: C 57 ARG cc_start: 0.7861 (ttm110) cc_final: 0.7492 (ttm110) REVERT: C 269 MET cc_start: 0.8141 (ttm) cc_final: 0.7684 (mtp) REVERT: E 57 ARG cc_start: 0.7885 (ttm110) cc_final: 0.7455 (ttm110) REVERT: E 293 MET cc_start: 0.9109 (mmt) cc_final: 0.8694 (mmt) REVERT: F 377 LYS cc_start: 0.8701 (ttmt) cc_final: 0.8102 (ttmm) REVERT: F 439 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7347 (tm-30) REVERT: G 105 GLN cc_start: 0.8811 (pp30) cc_final: 0.7931 (pp30) REVERT: G 144 ASP cc_start: 0.7262 (t0) cc_final: 0.7004 (t0) REVERT: H 24 ARG cc_start: 0.8421 (ttm110) cc_final: 0.8114 (ttm110) REVERT: H 138 ASN cc_start: 0.7967 (m110) cc_final: 0.7305 (m-40) REVERT: H 161 GLU cc_start: 0.8944 (pp20) cc_final: 0.8524 (pp20) REVERT: H 167 ASP cc_start: 0.8384 (t70) cc_final: 0.7965 (t0) REVERT: H 189 HIS cc_start: 0.7767 (m-70) cc_final: 0.7317 (m-70) REVERT: H 192 TYR cc_start: 0.7940 (m-10) cc_final: 0.7438 (m-10) REVERT: I 13 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8006 (mtmm) REVERT: I 46 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7884 (mt-10) REVERT: I 105 GLN cc_start: 0.8841 (pp30) cc_final: 0.7949 (pp30) REVERT: I 145 TYR cc_start: 0.7192 (p90) cc_final: 0.6575 (p90) REVERT: K 32 ASP cc_start: 0.8993 (p0) cc_final: 0.8703 (p0) REVERT: K 105 GLN cc_start: 0.8738 (pp30) cc_final: 0.7967 (pp30) REVERT: J 105 GLU cc_start: 0.7940 (tp30) cc_final: 0.7332 (tp30) REVERT: J 138 ASN cc_start: 0.8066 (m110) cc_final: 0.7611 (p0) REVERT: J 143 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7260 (pm20) REVERT: J 161 GLU cc_start: 0.8967 (pp20) cc_final: 0.8413 (pp20) REVERT: J 167 ASP cc_start: 0.8245 (t70) cc_final: 0.7939 (t0) REVERT: J 187 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8345 (mm-30) REVERT: J 190 LYS cc_start: 0.8197 (tptt) cc_final: 0.7893 (tppt) REVERT: L 24 ARG cc_start: 0.8318 (ttm110) cc_final: 0.8007 (ttm110) REVERT: L 36 TYR cc_start: 0.8968 (m-80) cc_final: 0.8612 (m-10) REVERT: L 138 ASN cc_start: 0.7928 (m110) cc_final: 0.7136 (m-40) REVERT: L 167 ASP cc_start: 0.8487 (t70) cc_final: 0.8287 (t0) REVERT: L 195 GLU cc_start: 0.6089 (tm-30) cc_final: 0.5741 (tp30) outliers start: 65 outliers final: 50 residues processed: 277 average time/residue: 0.3668 time to fit residues: 156.1830 Evaluate side-chains 262 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 209 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 477 LYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 278 CYS Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 482 CYS Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 209 PHE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 197 ASN Chi-restraints excluded: chain K residue 198 VAL Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 201 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 156 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 226 optimal weight: 20.0000 chunk 251 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 160 optimal weight: 10.0000 chunk 129 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.097821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.069025 restraints weight = 52283.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.071418 restraints weight = 23928.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.072898 restraints weight = 14940.050| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 22011 Z= 0.239 Angle : 0.661 9.749 29907 Z= 0.344 Chirality : 0.045 0.147 3312 Planarity : 0.004 0.068 3855 Dihedral : 5.179 40.547 3009 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.74 % Allowed : 17.81 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % 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: -0.10 (0.16), residues: 2724 helix: 1.89 (0.24), residues: 402 sheet: 0.32 (0.18), residues: 888 loop : -0.89 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 148 HIS 0.010 0.001 HIS J 198 PHE 0.026 0.002 PHE J 118 TYR 0.018 0.001 TYR E 102 ARG 0.006 0.000 ARG J 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00163 ( 3) link_NAG-ASN : angle 2.43539 ( 9) hydrogen bonds : bond 0.04306 ( 879) hydrogen bonds : angle 5.04732 ( 2493) SS BOND : bond 0.00451 ( 18) SS BOND : angle 1.94658 ( 36) covalent geometry : bond 0.00553 (21990) covalent geometry : angle 0.65711 (29862) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 221 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 477 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8632 (tppt) REVERT: C 28 VAL cc_start: 0.8982 (OUTLIER) cc_final: 0.8777 (p) REVERT: C 57 ARG cc_start: 0.7915 (ttm110) cc_final: 0.7589 (ttm110) REVERT: C 269 MET cc_start: 0.8186 (ttm) cc_final: 0.7692 (mtp) REVERT: E 293 MET cc_start: 0.9104 (mmt) cc_final: 0.8670 (mmt) REVERT: F 377 LYS cc_start: 0.8645 (ttmt) cc_final: 0.8058 (ttmm) REVERT: F 439 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7357 (tm-30) REVERT: G 117 LYS cc_start: 0.8274 (mmtt) cc_final: 0.8055 (mmtt) REVERT: H 24 ARG cc_start: 0.8458 (ttm110) cc_final: 0.8103 (ttm110) REVERT: H 138 ASN cc_start: 0.7966 (m110) cc_final: 0.7323 (m-40) REVERT: H 161 GLU cc_start: 0.8897 (pp20) cc_final: 0.8438 (pp20) REVERT: H 167 ASP cc_start: 0.8411 (t70) cc_final: 0.7943 (t0) REVERT: H 170 ASP cc_start: 0.7491 (t0) cc_final: 0.7290 (t0) REVERT: H 189 HIS cc_start: 0.7744 (m-70) cc_final: 0.7270 (m-70) REVERT: H 192 TYR cc_start: 0.7783 (m-10) cc_final: 0.7260 (m-10) REVERT: I 13 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7918 (mtmm) REVERT: I 105 GLN cc_start: 0.8842 (pp30) cc_final: 0.7901 (pp30) REVERT: I 145 TYR cc_start: 0.6953 (p90) cc_final: 0.6432 (p90) REVERT: K 32 ASP cc_start: 0.9056 (p0) cc_final: 0.8717 (p0) REVERT: K 196 CYS cc_start: 0.7683 (t) cc_final: 0.6413 (p) REVERT: J 105 GLU cc_start: 0.7826 (tp30) cc_final: 0.7208 (tp30) REVERT: J 138 ASN cc_start: 0.7999 (m110) cc_final: 0.7443 (p0) REVERT: J 161 GLU cc_start: 0.8953 (pp20) cc_final: 0.8370 (pp20) REVERT: J 167 ASP cc_start: 0.8334 (t70) cc_final: 0.7964 (t0) REVERT: J 187 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8421 (mm-30) REVERT: L 36 TYR cc_start: 0.8934 (m-80) cc_final: 0.8585 (m-10) REVERT: L 138 ASN cc_start: 0.7955 (m110) cc_final: 0.7169 (m-40) REVERT: L 161 GLU cc_start: 0.8807 (pp20) cc_final: 0.8395 (pp20) REVERT: L 167 ASP cc_start: 0.8413 (t70) cc_final: 0.8208 (t0) REVERT: L 195 GLU cc_start: 0.6248 (tm-30) cc_final: 0.5930 (tp30) outliers start: 66 outliers final: 57 residues processed: 279 average time/residue: 0.3437 time to fit residues: 145.5858 Evaluate side-chains 270 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 210 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 477 LYS Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 278 CYS Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 482 CYS Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 209 PHE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 70 ASN Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 197 ASN Chi-restraints excluded: chain K residue 198 VAL Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 201 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 28 optimal weight: 0.6980 chunk 163 optimal weight: 9.9990 chunk 183 optimal weight: 20.0000 chunk 239 optimal weight: 0.9980 chunk 245 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 169 optimal weight: 0.9980 chunk 144 optimal weight: 0.0980 chunk 266 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 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 = 0.3668 r_free = 0.3668 target = 0.104493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.076281 restraints weight = 51708.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.078833 restraints weight = 23755.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.080444 restraints weight = 14645.630| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22011 Z= 0.123 Angle : 0.596 10.068 29907 Z= 0.310 Chirality : 0.044 0.148 3312 Planarity : 0.004 0.068 3855 Dihedral : 4.841 38.970 3009 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.24 % Allowed : 18.35 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % 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: -0.00 (0.16), residues: 2724 helix: 2.01 (0.25), residues: 408 sheet: 0.39 (0.18), residues: 870 loop : -0.84 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 148 HIS 0.011 0.001 HIS J 198 PHE 0.027 0.001 PHE J 118 TYR 0.015 0.001 TYR J 173 ARG 0.007 0.000 ARG J 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 3) link_NAG-ASN : angle 2.33964 ( 9) hydrogen bonds : bond 0.03764 ( 879) hydrogen bonds : angle 4.78641 ( 2493) SS BOND : bond 0.00263 ( 18) SS BOND : angle 1.44029 ( 36) covalent geometry : bond 0.00280 (21990) covalent geometry : angle 0.59297 (29862) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 239 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8287 (ttm110) cc_final: 0.7904 (ttm110) REVERT: B 451 ASN cc_start: 0.8210 (m-40) cc_final: 0.7920 (t0) REVERT: B 477 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8473 (tppt) REVERT: C 57 ARG cc_start: 0.7746 (ttm110) cc_final: 0.7404 (ttm110) REVERT: C 269 MET cc_start: 0.8062 (ttm) cc_final: 0.7686 (mtp) REVERT: D 392 LYS cc_start: 0.8943 (tppt) cc_final: 0.8533 (ttmm) REVERT: D 396 GLN cc_start: 0.7940 (tt0) cc_final: 0.7536 (pt0) REVERT: E 57 ARG cc_start: 0.7812 (ttm110) cc_final: 0.7473 (ttm110) REVERT: E 293 MET cc_start: 0.9108 (mmt) cc_final: 0.8637 (mmt) REVERT: F 353 ASP cc_start: 0.7983 (p0) cc_final: 0.7551 (p0) REVERT: F 424 ASP cc_start: 0.7714 (t0) cc_final: 0.7484 (t0) REVERT: F 439 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7258 (tm-30) REVERT: G 105 GLN cc_start: 0.8604 (pp30) cc_final: 0.7736 (pp30) REVERT: G 117 LYS cc_start: 0.8296 (mmtt) cc_final: 0.8086 (mmtt) REVERT: G 196 CYS cc_start: 0.5833 (t) cc_final: 0.5605 (p) REVERT: H 24 ARG cc_start: 0.8466 (ttm110) cc_final: 0.8189 (ttm110) REVERT: H 138 ASN cc_start: 0.7907 (m110) cc_final: 0.7354 (m-40) REVERT: H 161 GLU cc_start: 0.8894 (pp20) cc_final: 0.8484 (pp20) REVERT: H 167 ASP cc_start: 0.8462 (t70) cc_final: 0.8037 (t0) REVERT: H 189 HIS cc_start: 0.7655 (m-70) cc_final: 0.7104 (m-70) REVERT: H 192 TYR cc_start: 0.7739 (m-10) cc_final: 0.7253 (m-10) REVERT: I 13 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8023 (mtmm) REVERT: I 46 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7978 (mt-10) REVERT: I 105 GLN cc_start: 0.8695 (pp30) cc_final: 0.7751 (pp30) REVERT: I 145 TYR cc_start: 0.6836 (p90) cc_final: 0.6385 (p90) REVERT: K 32 ASP cc_start: 0.8925 (p0) cc_final: 0.8635 (p0) REVERT: K 97 VAL cc_start: 0.8324 (p) cc_final: 0.8121 (m) REVERT: K 100 ASN cc_start: 0.8509 (m-40) cc_final: 0.8140 (m-40) REVERT: K 105 GLN cc_start: 0.8646 (pp30) cc_final: 0.7774 (pp30) REVERT: K 154 TRP cc_start: 0.8305 (m100) cc_final: 0.8085 (m100) REVERT: J 105 GLU cc_start: 0.7752 (tp30) cc_final: 0.7351 (tp30) REVERT: J 138 ASN cc_start: 0.7873 (m110) cc_final: 0.7200 (m-40) REVERT: J 161 GLU cc_start: 0.8935 (pp20) cc_final: 0.8352 (pp20) REVERT: J 167 ASP cc_start: 0.8448 (t70) cc_final: 0.8178 (t0) REVERT: J 187 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8396 (mm-30) REVERT: L 36 TYR cc_start: 0.8908 (m-80) cc_final: 0.8592 (m-10) REVERT: L 138 ASN cc_start: 0.7835 (m110) cc_final: 0.7072 (m-40) REVERT: L 142 ARG cc_start: 0.8357 (mmt-90) cc_final: 0.8091 (tpp-160) REVERT: L 161 GLU cc_start: 0.8766 (pp20) cc_final: 0.8394 (pp20) REVERT: L 195 GLU cc_start: 0.6212 (tm-30) cc_final: 0.5920 (tp30) outliers start: 54 outliers final: 47 residues processed: 287 average time/residue: 0.3406 time to fit residues: 147.6468 Evaluate side-chains 270 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 221 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 477 LYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 278 CYS Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 482 CYS Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 209 PHE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 197 ASN Chi-restraints excluded: chain K residue 198 VAL Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 201 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 117 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 217 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 168 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 HIS ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 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 = 0.3612 r_free = 0.3612 target = 0.101123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.072834 restraints weight = 51788.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.075285 restraints weight = 23792.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.076833 restraints weight = 14784.736| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22011 Z= 0.119 Angle : 0.592 9.719 29907 Z= 0.307 Chirality : 0.043 0.166 3312 Planarity : 0.004 0.066 3855 Dihedral : 4.669 36.895 3009 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.12 % Allowed : 18.64 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % 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: 0.09 (0.16), residues: 2724 helix: 2.15 (0.25), residues: 408 sheet: 0.39 (0.18), residues: 876 loop : -0.77 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 148 HIS 0.010 0.001 HIS J 198 PHE 0.027 0.001 PHE J 118 TYR 0.016 0.001 TYR D 496 ARG 0.007 0.000 ARG J 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00181 ( 3) link_NAG-ASN : angle 2.21217 ( 9) hydrogen bonds : bond 0.03620 ( 879) hydrogen bonds : angle 4.70672 ( 2493) SS BOND : bond 0.00258 ( 18) SS BOND : angle 1.38439 ( 36) covalent geometry : bond 0.00271 (21990) covalent geometry : angle 0.58922 (29862) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7077.82 seconds wall clock time: 125 minutes 15.41 seconds (7515.41 seconds total)