Starting phenix.real_space_refine on Mon Aug 25 20:35:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vue_43529/08_2025/8vue_43529.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vue_43529/08_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_43529/08_2025/8vue_43529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vue_43529/08_2025/8vue_43529.map" model { file = "/net/cci-nas-00/data/ceres_data/8vue_43529/08_2025/8vue_43529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vue_43529/08_2025/8vue_43529.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: C, E, D, F, I, K, J, L Time building chain proxies: 4.47, per 1000 atoms: 0.21 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: 2.15 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.18 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: 4.78 Time building geometry restraints manager: 2.77 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.790 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.260 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.001 ARG L 108 TYR 0.018 0.002 TYR B 358 PHE 0.017 0.002 PHE J 118 TRP 0.012 0.002 TRP K 35A HIS 0.005 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00724 (21990) covalent geometry : angle 0.94083 (29862) SS BOND : bond 0.01535 ( 18) SS BOND : angle 3.30269 ( 36) hydrogen bonds : bond 0.13923 ( 879) hydrogen bonds : angle 7.24403 ( 2493) link_NAG-ASN : bond 0.00132 ( 3) link_NAG-ASN : angle 3.17607 ( 9) *********************** 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 : 0.890 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: 0.1939 time to fit residues: 141.2436 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 : 0.930 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 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 77 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 I 192 GLN I 197 ASN I 204 ASN K 6 GLN K 155 ASN K 192 GLN 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: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.107334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.078450 restraints weight = 51566.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.081045 restraints weight = 23987.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.082693 restraints weight = 14892.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.083691 restraints weight = 10986.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.084374 restraints weight = 9094.890| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22011 Z= 0.163 Angle : 0.650 7.886 29907 Z= 0.346 Chirality : 0.046 0.159 3312 Planarity : 0.005 0.077 3855 Dihedral : 6.188 45.797 3063 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.66 % Allowed : 12.08 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.16), residues: 2724 helix: 1.26 (0.25), residues: 402 sheet: -0.27 (0.17), residues: 870 loop : -1.51 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 43 TYR 0.028 0.001 TYR J 140 PHE 0.028 0.002 PHE I 122 TRP 0.013 0.001 TRP J 148 HIS 0.010 0.002 HIS H 198 Details of bonding type rmsd covalent geometry : bond 0.00372 (21990) covalent geometry : angle 0.64599 (29862) SS BOND : bond 0.00297 ( 18) SS BOND : angle 1.93325 ( 36) hydrogen bonds : bond 0.04467 ( 879) hydrogen bonds : angle 5.48017 ( 2493) link_NAG-ASN : bond 0.00340 ( 3) link_NAG-ASN : angle 1.97143 ( 9) *********************** 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: 64 poor density : 279 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.9069 (mmt) cc_final: 0.8500 (mmt) REVERT: C 305 GLU cc_start: 0.7749 (mp0) cc_final: 0.7345 (pp20) REVERT: D 437 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8033 (mm-30) REVERT: E 241 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8171 (t0) REVERT: G 144 ASP cc_start: 0.7038 (t0) cc_final: 0.6727 (t0) REVERT: G 154 TRP cc_start: 0.7878 (m100) cc_final: 0.7187 (m100) REVERT: G 196 CYS cc_start: 0.7567 (OUTLIER) cc_final: 0.6436 (p) REVERT: G 209 LYS cc_start: 0.7991 (tppt) cc_final: 0.7523 (mmtp) REVERT: H 24 ARG cc_start: 0.8224 (ttm110) cc_final: 0.7812 (ttm110) REVERT: H 30 SER cc_start: 0.9213 (t) cc_final: 0.8980 (p) REVERT: H 36 TYR cc_start: 0.8882 (m-80) cc_final: 0.8516 (m-10) REVERT: H 118 PHE cc_start: 0.7561 (m-80) cc_final: 0.7016 (m-80) REVERT: H 138 ASN cc_start: 0.8243 (m-40) cc_final: 0.7672 (t0) REVERT: H 142 ARG cc_start: 0.8754 (ttt-90) cc_final: 0.8257 (mmm-85) REVERT: H 190 LYS cc_start: 0.8018 (tptt) cc_final: 0.7475 (tppt) REVERT: I 85 GLU cc_start: 0.8234 (mp0) cc_final: 0.7966 (mp0) REVERT: I 154 TRP cc_start: 0.7728 (m100) cc_final: 0.6857 (m100) REVERT: I 209 LYS cc_start: 0.8026 (tppt) cc_final: 0.7755 (mmtm) REVERT: K 144 ASP cc_start: 0.7168 (t0) cc_final: 0.6922 (t0) REVERT: K 166 PHE cc_start: 0.7752 (m-10) cc_final: 0.7362 (m-10) REVERT: K 179 SER cc_start: 0.6967 (OUTLIER) cc_final: 0.6496 (p) REVERT: K 196 CYS cc_start: 0.7381 (t) cc_final: 0.7111 (p) REVERT: K 209 LYS cc_start: 0.8363 (tppt) cc_final: 0.8151 (mmtp) REVERT: J 118 PHE cc_start: 0.7089 (m-10) cc_final: 0.6719 (m-10) REVERT: J 142 ARG cc_start: 0.8535 (tpp80) cc_final: 0.8068 (mmm-85) REVERT: J 189 HIS cc_start: 0.8270 (m90) cc_final: 0.7983 (m90) REVERT: J 190 LYS cc_start: 0.8133 (tptt) cc_final: 0.7488 (tppt) REVERT: L 24 ARG cc_start: 0.8353 (ttm110) cc_final: 0.7995 (ttm-80) REVERT: L 30 SER cc_start: 0.9228 (t) cc_final: 0.8973 (p) REVERT: L 36 TYR cc_start: 0.8950 (m-80) cc_final: 0.8739 (m-10) REVERT: L 106 ILE cc_start: 0.7915 (mm) cc_final: 0.7634 (mm) REVERT: L 142 ARG cc_start: 0.8595 (tpp80) cc_final: 0.8063 (mmm160) REVERT: L 190 LYS cc_start: 0.8038 (tptt) cc_final: 0.7770 (tppt) outliers start: 64 outliers final: 28 residues processed: 328 average time/residue: 0.1758 time to fit residues: 87.7952 Evaluate side-chains 249 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 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 241 ASP Chi-restraints excluded: chain G residue 100 LEU 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 114 SER Chi-restraints excluded: chain H residue 115 VAL 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 216 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 267 optimal weight: 0.7980 chunk 260 optimal weight: 0.6980 chunk 238 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 268 optimal weight: 5.9990 chunk 227 optimal weight: 20.0000 chunk 175 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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** F 359 HIS ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100EASN G 197 ASN H 38 GLN H 124 GLN I 197 ASN K 6 GLN K 65 ASN K 197 ASN J 147 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.105304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.076350 restraints weight = 52140.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.078874 restraints weight = 24236.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.080469 restraints weight = 15092.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.081484 restraints weight = 11210.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.082078 restraints weight = 9272.932| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22011 Z= 0.189 Angle : 0.626 8.349 29907 Z= 0.330 Chirality : 0.045 0.167 3312 Planarity : 0.005 0.072 3855 Dihedral : 5.264 39.331 3014 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.57 % Allowed : 14.90 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.16), residues: 2724 helix: 1.62 (0.25), residues: 402 sheet: 0.09 (0.18), residues: 864 loop : -1.29 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 212 TYR 0.013 0.001 TYR J 140 PHE 0.019 0.002 PHE H 139 TRP 0.010 0.001 TRP J 148 HIS 0.007 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00435 (21990) covalent geometry : angle 0.62178 (29862) SS BOND : bond 0.00465 ( 18) SS BOND : angle 1.95853 ( 36) hydrogen bonds : bond 0.04369 ( 879) hydrogen bonds : angle 5.18347 ( 2493) link_NAG-ASN : bond 0.00253 ( 3) link_NAG-ASN : angle 2.14645 ( 9) *********************** 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 298 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 236 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.9073 (mmt) cc_final: 0.8540 (mmt) REVERT: C 293 MET cc_start: 0.9085 (mmt) cc_final: 0.8762 (mmt) REVERT: C 305 GLU cc_start: 0.7763 (mp0) cc_final: 0.7445 (pp20) REVERT: D 437 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7918 (mm-30) REVERT: E 293 MET cc_start: 0.9112 (mmt) cc_final: 0.8675 (mmt) REVERT: G 144 ASP cc_start: 0.6971 (t0) cc_final: 0.6688 (t0) REVERT: G 154 TRP cc_start: 0.7945 (m100) cc_final: 0.7728 (m100) REVERT: G 176 TYR cc_start: 0.8047 (m-80) cc_final: 0.7834 (m-80) REVERT: G 196 CYS cc_start: 0.7509 (OUTLIER) cc_final: 0.6702 (p) REVERT: G 209 LYS cc_start: 0.8049 (tppt) cc_final: 0.7570 (mmtp) REVERT: H 36 TYR cc_start: 0.8962 (m-80) cc_final: 0.8740 (m-80) REVERT: H 118 PHE cc_start: 0.7458 (m-80) cc_final: 0.6937 (m-10) REVERT: H 138 ASN cc_start: 0.8058 (m-40) cc_final: 0.7578 (t0) REVERT: H 187 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8340 (mm-30) REVERT: H 189 HIS cc_start: 0.8065 (m-70) cc_final: 0.7674 (m-70) REVERT: H 190 LYS cc_start: 0.8035 (tptt) cc_final: 0.7697 (tppt) REVERT: H 192 TYR cc_start: 0.8519 (m-10) cc_final: 0.8100 (m-10) REVERT: I 154 TRP cc_start: 0.7803 (m100) cc_final: 0.6620 (m100) REVERT: I 209 LYS cc_start: 0.7860 (tppt) cc_final: 0.7514 (mmmm) REVERT: K 46 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8213 (mt-10) REVERT: K 100 ASN cc_start: 0.8779 (m-40) cc_final: 0.8339 (m-40) REVERT: K 105 GLN cc_start: 0.8800 (pp30) cc_final: 0.7890 (pp30) REVERT: K 144 ASP cc_start: 0.7179 (t0) cc_final: 0.6922 (t0) REVERT: K 166 PHE cc_start: 0.7908 (m-80) cc_final: 0.7595 (m-10) REVERT: K 196 CYS cc_start: 0.7948 (t) cc_final: 0.6924 (p) REVERT: K 209 LYS cc_start: 0.8413 (tppt) cc_final: 0.8167 (mmtp) REVERT: J 118 PHE cc_start: 0.7057 (m-80) cc_final: 0.6850 (m-10) REVERT: J 142 ARG cc_start: 0.8512 (tpp80) cc_final: 0.7739 (mmm-85) REVERT: J 143 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7457 (pm20) REVERT: J 187 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8351 (mt-10) REVERT: J 190 LYS cc_start: 0.7930 (tptt) cc_final: 0.7498 (tppt) REVERT: L 36 TYR cc_start: 0.8892 (m-80) cc_final: 0.8666 (m-10) REVERT: L 108 ARG cc_start: 0.8220 (ptm160) cc_final: 0.8015 (ptm160) REVERT: L 142 ARG cc_start: 0.8696 (tpp80) cc_final: 0.8144 (mmm160) outliers start: 62 outliers final: 38 residues processed: 279 average time/residue: 0.1720 time to fit residues: 73.6021 Evaluate side-chains 253 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR 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 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 115 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 201 LEU 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 220 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 256 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 186 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 299 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 171 GLN K 197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.105123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.075833 restraints weight = 51915.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.078342 restraints weight = 24043.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.079960 restraints weight = 15055.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.080995 restraints weight = 11191.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.081598 restraints weight = 9257.307| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22011 Z= 0.173 Angle : 0.596 8.680 29907 Z= 0.313 Chirality : 0.044 0.157 3312 Planarity : 0.004 0.073 3855 Dihedral : 5.042 39.689 3009 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.07 % Allowed : 15.19 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.16), residues: 2724 helix: 1.79 (0.25), residues: 408 sheet: 0.24 (0.18), residues: 864 loop : -1.16 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 142 TYR 0.021 0.001 TYR E 141 PHE 0.018 0.002 PHE L 139 TRP 0.011 0.001 TRP J 148 HIS 0.006 0.001 HIS J 198 Details of bonding type rmsd covalent geometry : bond 0.00397 (21990) covalent geometry : angle 0.59221 (29862) SS BOND : bond 0.00373 ( 18) SS BOND : angle 1.71476 ( 36) hydrogen bonds : bond 0.04190 ( 879) hydrogen bonds : angle 4.98635 ( 2493) link_NAG-ASN : bond 0.00243 ( 3) link_NAG-ASN : angle 2.10151 ( 9) *********************** 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 316 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 242 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.9051 (mmt) cc_final: 0.8529 (mmt) REVERT: C 28 VAL cc_start: 0.9094 (OUTLIER) cc_final: 0.8869 (p) REVERT: C 293 MET cc_start: 0.9085 (mmt) cc_final: 0.8746 (mmt) REVERT: D 353 ASP cc_start: 0.8029 (p0) cc_final: 0.7785 (p0) REVERT: E 286 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7782 (ptp) REVERT: E 293 MET cc_start: 0.9094 (mmt) cc_final: 0.8658 (mmt) REVERT: F 424 ASP cc_start: 0.7811 (t0) cc_final: 0.7602 (t0) REVERT: G 105 GLN cc_start: 0.8774 (pp30) cc_final: 0.8501 (pp30) REVERT: G 144 ASP cc_start: 0.7117 (t0) cc_final: 0.6813 (t0) REVERT: G 171 GLN cc_start: 0.8095 (tm130) cc_final: 0.7266 (mt0) REVERT: G 192 GLN cc_start: 0.5274 (OUTLIER) cc_final: 0.4569 (mm110) REVERT: G 196 CYS cc_start: 0.7641 (t) cc_final: 0.6701 (p) REVERT: G 209 LYS cc_start: 0.7914 (tppt) cc_final: 0.7482 (mmtp) REVERT: H 24 ARG cc_start: 0.8415 (ttm110) cc_final: 0.7995 (ttm110) REVERT: H 118 PHE cc_start: 0.7401 (m-80) cc_final: 0.6985 (m-10) REVERT: H 138 ASN cc_start: 0.7958 (m-40) cc_final: 0.7550 (t0) REVERT: H 189 HIS cc_start: 0.7669 (m-70) cc_final: 0.7424 (m-70) REVERT: I 105 GLN cc_start: 0.8778 (pp30) cc_final: 0.7982 (pp30) REVERT: I 154 TRP cc_start: 0.7811 (m100) cc_final: 0.6752 (m100) REVERT: I 176 TYR cc_start: 0.8134 (m-80) cc_final: 0.7926 (m-80) REVERT: I 209 LYS cc_start: 0.7975 (tppt) cc_final: 0.7759 (mmtp) REVERT: K 32 ASP cc_start: 0.8879 (p0) cc_final: 0.8600 (p0) REVERT: K 105 GLN cc_start: 0.8741 (pp30) cc_final: 0.7926 (pp30) REVERT: K 166 PHE cc_start: 0.7940 (m-80) cc_final: 0.7630 (m-10) REVERT: K 176 TYR cc_start: 0.8145 (m-80) cc_final: 0.7929 (m-80) REVERT: K 192 GLN cc_start: 0.4454 (OUTLIER) cc_final: 0.3487 (mm110) REVERT: J 116 PHE cc_start: 0.8043 (m-10) cc_final: 0.7814 (m-10) REVERT: J 142 ARG cc_start: 0.8599 (tpp80) cc_final: 0.7756 (mmm-85) REVERT: J 143 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7379 (pm20) REVERT: J 190 LYS cc_start: 0.7943 (tptt) cc_final: 0.7645 (tppt) REVERT: L 24 ARG cc_start: 0.8371 (ttm110) cc_final: 0.8113 (ttm110) REVERT: L 30 SER cc_start: 0.9149 (t) cc_final: 0.8751 (p) REVERT: L 36 TYR cc_start: 0.8891 (m-80) cc_final: 0.8606 (m-10) REVERT: L 148 TRP cc_start: 0.5558 (m100) cc_final: 0.5350 (m100) REVERT: L 195 GLU cc_start: 0.6498 (tm-30) cc_final: 0.6260 (tp30) outliers start: 74 outliers final: 47 residues processed: 305 average time/residue: 0.1697 time to fit residues: 78.6777 Evaluate side-chains 265 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 213 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 29 THR 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 28 VAL 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 C residue 303 ILE Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain E residue 24 MET 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 286 MET 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 108 LEU Chi-restraints excluded: chain G residue 165 THR 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 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 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 142 VAL Chi-restraints excluded: chain K residue 192 GLN 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 J residue 171 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 52 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 246 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.107000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.078211 restraints weight = 52074.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.080659 restraints weight = 23955.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.082269 restraints weight = 14929.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.083226 restraints weight = 11048.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.083901 restraints weight = 9186.075| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22011 Z= 0.159 Angle : 0.587 8.481 29907 Z= 0.307 Chirality : 0.044 0.152 3312 Planarity : 0.004 0.071 3855 Dihedral : 4.908 38.650 3009 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.32 % Allowed : 16.15 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.16), residues: 2724 helix: 1.94 (0.25), residues: 408 sheet: 0.34 (0.18), residues: 864 loop : -1.07 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 142 TYR 0.018 0.001 TYR E 141 PHE 0.021 0.002 PHE I 122 TRP 0.013 0.001 TRP H 148 HIS 0.006 0.001 HIS J 198 Details of bonding type rmsd covalent geometry : bond 0.00364 (21990) covalent geometry : angle 0.58299 (29862) SS BOND : bond 0.00352 ( 18) SS BOND : angle 1.65738 ( 36) hydrogen bonds : bond 0.04037 ( 879) hydrogen bonds : angle 4.88593 ( 2493) link_NAG-ASN : bond 0.00230 ( 3) link_NAG-ASN : angle 2.17452 ( 9) *********************** 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 321 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 241 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.9052 (mmt) cc_final: 0.8500 (mmt) REVERT: B 477 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8539 (tppt) REVERT: C 28 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8862 (p) REVERT: C 269 MET cc_start: 0.8200 (ttm) cc_final: 0.7873 (mtp) REVERT: C 293 MET cc_start: 0.9061 (mmt) cc_final: 0.8716 (mmt) REVERT: D 353 ASP cc_start: 0.8026 (p0) cc_final: 0.7795 (p0) REVERT: D 446 ASP cc_start: 0.8479 (t70) cc_final: 0.7935 (t0) REVERT: E 57 ARG cc_start: 0.7819 (ttm110) cc_final: 0.7593 (ttm110) REVERT: E 293 MET cc_start: 0.9092 (mmt) cc_final: 0.8636 (mmt) REVERT: F 439 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7273 (tm-30) REVERT: G 105 GLN cc_start: 0.8685 (pp30) cc_final: 0.8375 (pp30) REVERT: G 143 LYS cc_start: 0.8034 (tppt) cc_final: 0.7753 (mmmt) REVERT: G 144 ASP cc_start: 0.7021 (t0) cc_final: 0.6728 (t0) REVERT: G 154 TRP cc_start: 0.8016 (m100) cc_final: 0.7342 (m100) REVERT: G 192 GLN cc_start: 0.5737 (OUTLIER) cc_final: 0.5391 (mm110) REVERT: G 196 CYS cc_start: 0.7674 (t) cc_final: 0.6711 (p) REVERT: G 209 LYS cc_start: 0.7857 (tppt) cc_final: 0.7398 (mmtp) REVERT: H 24 ARG cc_start: 0.8412 (ttm110) cc_final: 0.8156 (ttm110) REVERT: H 138 ASN cc_start: 0.8090 (m-40) cc_final: 0.7625 (t0) REVERT: H 161 GLU cc_start: 0.8897 (pp20) cc_final: 0.8497 (pp20) REVERT: H 189 HIS cc_start: 0.7852 (m-70) cc_final: 0.7478 (m-70) REVERT: I 3 GLN cc_start: 0.8061 (mp10) cc_final: 0.7846 (mp10) REVERT: I 105 GLN cc_start: 0.8765 (pp30) cc_final: 0.7976 (pp30) REVERT: I 122 PHE cc_start: 0.8327 (m-10) cc_final: 0.8037 (m-80) REVERT: I 176 TYR cc_start: 0.8181 (m-80) cc_final: 0.7924 (m-80) REVERT: I 210 LYS cc_start: 0.6734 (tptt) cc_final: 0.6023 (tppt) REVERT: K 32 ASP cc_start: 0.8889 (p0) cc_final: 0.8616 (p0) REVERT: K 105 GLN cc_start: 0.8694 (pp30) cc_final: 0.7887 (pp30) REVERT: K 154 TRP cc_start: 0.8205 (m100) cc_final: 0.7942 (m100) REVERT: K 166 PHE cc_start: 0.7906 (m-80) cc_final: 0.7581 (m-10) REVERT: K 192 GLN cc_start: 0.4227 (OUTLIER) cc_final: 0.3304 (mm110) REVERT: J 143 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7354 (pm20) REVERT: J 190 LYS cc_start: 0.7996 (tptt) cc_final: 0.7717 (tppt) REVERT: L 24 ARG cc_start: 0.8348 (ttm110) cc_final: 0.7947 (ttm110) REVERT: L 30 SER cc_start: 0.9045 (t) cc_final: 0.8615 (p) REVERT: L 36 TYR cc_start: 0.8894 (m-80) cc_final: 0.8576 (m-10) REVERT: L 195 GLU cc_start: 0.6419 (tm-30) cc_final: 0.6026 (tp30) outliers start: 80 outliers final: 55 residues processed: 308 average time/residue: 0.1715 time to fit residues: 80.9179 Evaluate side-chains 278 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 218 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 278 CYS Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 436 MET 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 356 TYR Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain E residue 24 MET 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 99 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 165 THR 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 G residue 198 VAL 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 146 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 201 LEU 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 192 GLN 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 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 264 optimal weight: 9.9990 chunk 246 optimal weight: 7.9990 chunk 175 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 251 optimal weight: 10.0000 chunk 171 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 253 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 227 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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** C 150 ASN ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 GLN I 100EASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.103385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.074745 restraints weight = 52989.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.077119 restraints weight = 24533.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.078651 restraints weight = 15355.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.079602 restraints weight = 11412.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.080144 restraints weight = 9508.032| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 22011 Z= 0.321 Angle : 0.716 9.462 29907 Z= 0.373 Chirality : 0.047 0.180 3312 Planarity : 0.005 0.073 3855 Dihedral : 5.454 40.748 3009 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.57 % Allowed : 16.77 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.16), residues: 2724 helix: 1.63 (0.24), residues: 402 sheet: 0.14 (0.18), residues: 894 loop : -1.16 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 24 TYR 0.019 0.002 TYR E 102 PHE 0.024 0.002 PHE H 118 TRP 0.011 0.002 TRP B 426 HIS 0.007 0.002 HIS J 198 Details of bonding type rmsd covalent geometry : bond 0.00741 (21990) covalent geometry : angle 0.71067 (29862) SS BOND : bond 0.00514 ( 18) SS BOND : angle 2.26981 ( 36) hydrogen bonds : bond 0.04791 ( 879) hydrogen bonds : angle 5.28983 ( 2493) link_NAG-ASN : bond 0.00136 ( 3) link_NAG-ASN : angle 2.59458 ( 9) *********************** 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 310 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 224 time to evaluate : 0.909 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: 0.8995 (mmt) cc_final: 0.8538 (mmt) REVERT: B 377 LYS cc_start: 0.8638 (ttmt) cc_final: 0.8145 (ttmm) REVERT: C 28 VAL cc_start: 0.9081 (OUTLIER) cc_final: 0.8873 (p) REVERT: C 269 MET cc_start: 0.8209 (ttm) cc_final: 0.7871 (mtp) REVERT: C 293 MET cc_start: 0.8998 (mmt) cc_final: 0.8718 (mmt) REVERT: E 293 MET cc_start: 0.9023 (mmt) cc_final: 0.8585 (mmt) REVERT: F 377 LYS cc_start: 0.8709 (ttmt) cc_final: 0.8136 (ttmm) REVERT: F 439 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7408 (tm-30) REVERT: G 143 LYS cc_start: 0.7977 (tppt) cc_final: 0.7673 (mmmt) REVERT: G 144 ASP cc_start: 0.7292 (t0) cc_final: 0.7032 (t0) REVERT: G 196 CYS cc_start: 0.7806 (t) cc_final: 0.7028 (p) REVERT: H 24 ARG cc_start: 0.8395 (ttm110) cc_final: 0.8148 (ttm110) REVERT: H 138 ASN cc_start: 0.8098 (m-40) cc_final: 0.7632 (t0) REVERT: H 161 GLU cc_start: 0.8919 (pp20) cc_final: 0.8462 (pp20) REVERT: H 189 HIS cc_start: 0.7862 (m-70) cc_final: 0.7419 (m-70) REVERT: H 198 HIS cc_start: 0.4588 (OUTLIER) cc_final: 0.3575 (t-90) REVERT: I 122 PHE cc_start: 0.8264 (m-10) cc_final: 0.7938 (m-80) REVERT: I 145 TYR cc_start: 0.7052 (p90) cc_final: 0.6596 (p90) REVERT: K 32 ASP cc_start: 0.8998 (p0) cc_final: 0.8714 (p0) REVERT: K 105 GLN cc_start: 0.8826 (pp30) cc_final: 0.8056 (pp30) REVERT: K 117 LYS cc_start: 0.8291 (mmtt) cc_final: 0.8054 (mptt) REVERT: K 166 PHE cc_start: 0.7888 (m-80) cc_final: 0.7573 (m-10) REVERT: J 143 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7346 (pm20) REVERT: J 161 GLU cc_start: 0.8959 (pp20) cc_final: 0.8358 (pp20) REVERT: J 190 LYS cc_start: 0.8220 (tptt) cc_final: 0.7932 (tppt) REVERT: L 36 TYR cc_start: 0.8972 (m-80) cc_final: 0.8683 (m-10) REVERT: L 114 SER cc_start: 0.6579 (OUTLIER) cc_final: 0.6372 (t) REVERT: L 161 GLU cc_start: 0.8768 (pp20) cc_final: 0.8372 (pp20) REVERT: L 181 LEU cc_start: 0.7311 (pt) cc_final: 0.6556 (pt) REVERT: L 195 GLU cc_start: 0.6202 (tm-30) cc_final: 0.5769 (tp30) outliers start: 86 outliers final: 60 residues processed: 296 average time/residue: 0.1667 time to fit residues: 76.5717 Evaluate side-chains 271 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 207 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 261 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 436 MET Chi-restraints excluded: chain B residue 447 SER 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 142 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 108 LEU 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 70 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 G residue 198 VAL 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 163 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 198 HIS 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 70 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 85 THR Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 143 GLU 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 201 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 28 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 211 optimal weight: 0.8980 chunk 239 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 261 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 252 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100EASN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.107322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.079601 restraints weight = 51757.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.081998 restraints weight = 23266.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.083549 restraints weight = 14259.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.084529 restraints weight = 10471.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.085121 restraints weight = 8634.074| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22011 Z= 0.133 Angle : 0.590 8.931 29907 Z= 0.308 Chirality : 0.044 0.148 3312 Planarity : 0.004 0.074 3855 Dihedral : 4.980 39.983 3009 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.32 % Allowed : 18.56 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.16), residues: 2724 helix: 1.93 (0.25), residues: 408 sheet: 0.27 (0.18), residues: 894 loop : -1.00 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 142 TYR 0.010 0.001 TYR B 493 PHE 0.019 0.001 PHE J 118 TRP 0.012 0.001 TRP I 35A HIS 0.008 0.001 HIS J 198 Details of bonding type rmsd covalent geometry : bond 0.00298 (21990) covalent geometry : angle 0.58653 (29862) SS BOND : bond 0.00505 ( 18) SS BOND : angle 1.56590 ( 36) hydrogen bonds : bond 0.03950 ( 879) hydrogen bonds : angle 4.85230 ( 2493) link_NAG-ASN : bond 0.00213 ( 3) link_NAG-ASN : angle 2.37894 ( 9) *********************** 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 295 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 239 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 477 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8434 (tppt) REVERT: C 293 MET cc_start: 0.8978 (mmt) cc_final: 0.8658 (mmt) REVERT: D 446 ASP cc_start: 0.8477 (t70) cc_final: 0.7949 (t0) REVERT: E 57 ARG cc_start: 0.7787 (ttm110) cc_final: 0.7488 (ttm110) REVERT: E 293 MET cc_start: 0.9065 (mmt) cc_final: 0.8599 (mmt) REVERT: F 439 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7320 (tm-30) REVERT: G 171 GLN cc_start: 0.8158 (tm130) cc_final: 0.7926 (tm-30) REVERT: H 24 ARG cc_start: 0.8392 (ttm110) cc_final: 0.8112 (ttm110) REVERT: H 138 ASN cc_start: 0.7815 (m-40) cc_final: 0.7394 (t0) REVERT: H 142 ARG cc_start: 0.8612 (ttt-90) cc_final: 0.8172 (mtt-85) REVERT: H 161 GLU cc_start: 0.8883 (pp20) cc_final: 0.8469 (pp20) REVERT: H 189 HIS cc_start: 0.7808 (m-70) cc_final: 0.7297 (m-70) REVERT: I 81 GLN cc_start: 0.8446 (tt0) cc_final: 0.8165 (mt0) REVERT: I 100 ASN cc_start: 0.8418 (m-40) cc_final: 0.8201 (m-40) REVERT: I 105 GLN cc_start: 0.8777 (pp30) cc_final: 0.7916 (pp30) REVERT: I 122 PHE cc_start: 0.8295 (m-10) cc_final: 0.8000 (m-80) REVERT: K 32 ASP cc_start: 0.8902 (p0) cc_final: 0.8571 (p0) REVERT: K 100 ASN cc_start: 0.8466 (m-40) cc_final: 0.8126 (m-40) REVERT: K 105 GLN cc_start: 0.8685 (pp30) cc_final: 0.7896 (pp30) REVERT: K 117 LYS cc_start: 0.8287 (mmtt) cc_final: 0.8070 (mptt) REVERT: K 166 PHE cc_start: 0.7941 (m-80) cc_final: 0.7666 (m-10) REVERT: J 105 GLU cc_start: 0.8003 (tp30) cc_final: 0.7330 (tp30) REVERT: J 138 ASN cc_start: 0.7991 (m110) cc_final: 0.7596 (p0) REVERT: J 142 ARG cc_start: 0.8511 (tpp80) cc_final: 0.7837 (mmm-85) REVERT: J 143 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7298 (pm20) REVERT: J 161 GLU cc_start: 0.8935 (pp20) cc_final: 0.8392 (pp20) REVERT: L 36 TYR cc_start: 0.8934 (m-80) cc_final: 0.8578 (m-10) REVERT: L 138 ASN cc_start: 0.8008 (m110) cc_final: 0.7292 (t0) REVERT: L 142 ARG cc_start: 0.8732 (tpp80) cc_final: 0.8442 (mmt90) REVERT: L 161 GLU cc_start: 0.8719 (pp20) cc_final: 0.8353 (pp20) REVERT: L 170 ASP cc_start: 0.7159 (t0) cc_final: 0.6899 (t0) REVERT: L 195 GLU cc_start: 0.6365 (tm-30) cc_final: 0.5965 (tp30) outliers start: 56 outliers final: 47 residues processed: 283 average time/residue: 0.1754 time to fit residues: 75.9871 Evaluate side-chains 265 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 216 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU 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 436 MET Chi-restraints excluded: chain B residue 477 LYS Chi-restraints excluded: chain C residue 22 THR 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 E residue 24 MET 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 70 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 178 LEU Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain G residue 198 VAL 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 146 VAL Chi-restraints excluded: chain H residue 201 LEU 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 85 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 115 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 226 optimal weight: 7.9990 chunk 190 optimal weight: 3.9990 chunk 206 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 177 optimal weight: 8.9990 chunk 211 optimal weight: 0.8980 chunk 198 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 247 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 476 HIS ** C 32 HIS ** 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** ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.101249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.072809 restraints weight = 51930.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.075248 restraints weight = 24019.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.076790 restraints weight = 14978.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.077784 restraints weight = 11155.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.078330 restraints weight = 9219.183| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22011 Z= 0.234 Angle : 0.647 8.957 29907 Z= 0.338 Chirality : 0.045 0.152 3312 Planarity : 0.004 0.070 3855 Dihedral : 5.166 39.968 3009 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.95 % Allowed : 17.89 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.16), residues: 2724 helix: 1.90 (0.24), residues: 402 sheet: 0.23 (0.18), residues: 888 loop : -1.03 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 24 TYR 0.014 0.001 TYR E 102 PHE 0.018 0.002 PHE G 78 TRP 0.014 0.001 TRP B 426 HIS 0.008 0.001 HIS J 198 Details of bonding type rmsd covalent geometry : bond 0.00542 (21990) covalent geometry : angle 0.64223 (29862) SS BOND : bond 0.00411 ( 18) SS BOND : angle 2.03469 ( 36) hydrogen bonds : bond 0.04344 ( 879) hydrogen bonds : angle 5.06326 ( 2493) link_NAG-ASN : bond 0.00147 ( 3) link_NAG-ASN : angle 2.50860 ( 9) *********************** 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 294 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 223 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 377 LYS cc_start: 0.8621 (ttmt) cc_final: 0.8127 (ttmm) REVERT: B 477 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8470 (tppt) REVERT: C 293 MET cc_start: 0.8942 (mmt) cc_final: 0.8633 (mmt) REVERT: E 293 MET cc_start: 0.9050 (mmt) cc_final: 0.8637 (mmt) REVERT: F 377 LYS cc_start: 0.8692 (ttmt) cc_final: 0.8127 (ttmm) REVERT: F 439 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7297 (tm-30) REVERT: G 13 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8133 (mtmm) REVERT: H 24 ARG cc_start: 0.8385 (ttm110) cc_final: 0.8063 (ttm110) REVERT: H 138 ASN cc_start: 0.7954 (m-40) cc_final: 0.7506 (t0) REVERT: H 142 ARG cc_start: 0.8614 (ttt-90) cc_final: 0.8189 (mtt-85) REVERT: H 161 GLU cc_start: 0.8925 (pp20) cc_final: 0.8494 (pp20) REVERT: H 189 HIS cc_start: 0.7777 (m-70) cc_final: 0.7227 (m-70) REVERT: I 81 GLN cc_start: 0.8481 (tt0) cc_final: 0.8202 (mt0) REVERT: I 100 ASN cc_start: 0.8464 (m-40) cc_final: 0.8224 (m-40) REVERT: I 105 GLN cc_start: 0.8804 (pp30) cc_final: 0.7911 (pp30) REVERT: I 122 PHE cc_start: 0.8334 (m-10) cc_final: 0.8019 (m-80) REVERT: I 145 TYR cc_start: 0.7124 (p90) cc_final: 0.6640 (p90) REVERT: K 32 ASP cc_start: 0.8970 (p0) cc_final: 0.8676 (p0) REVERT: K 105 GLN cc_start: 0.8785 (pp30) cc_final: 0.7987 (pp30) REVERT: K 166 PHE cc_start: 0.7951 (m-80) cc_final: 0.7701 (m-10) REVERT: J 24 ARG cc_start: 0.8225 (ttm110) cc_final: 0.7786 (ttm110) REVERT: J 105 GLU cc_start: 0.8047 (tp30) cc_final: 0.7371 (tp30) REVERT: J 138 ASN cc_start: 0.8022 (m110) cc_final: 0.7640 (p0) REVERT: J 161 GLU cc_start: 0.8933 (pp20) cc_final: 0.8369 (pp20) REVERT: L 24 ARG cc_start: 0.8273 (ttm-80) cc_final: 0.7949 (ttm110) REVERT: L 36 TYR cc_start: 0.8982 (m-80) cc_final: 0.8637 (m-10) REVERT: L 138 ASN cc_start: 0.8041 (m110) cc_final: 0.7296 (t0) REVERT: L 161 GLU cc_start: 0.8762 (pp20) cc_final: 0.8381 (pp20) REVERT: L 170 ASP cc_start: 0.7221 (t0) cc_final: 0.6973 (t0) REVERT: L 195 GLU cc_start: 0.6203 (tm-30) cc_final: 0.5823 (tp30) outliers start: 71 outliers final: 58 residues processed: 285 average time/residue: 0.1713 time to fit residues: 75.2403 Evaluate side-chains 273 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 213 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 109 LEU 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 436 MET 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 142 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 E residue 29 THR Chi-restraints excluded: chain E residue 208 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 13 LYS 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 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 G residue 198 VAL 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 163 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 70 ASN 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 165 THR 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 70 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 85 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 201 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 155 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 247 optimal weight: 20.0000 chunk 244 optimal weight: 8.9990 chunk 162 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 230 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 171 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.105937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.078028 restraints weight = 51669.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.080435 restraints weight = 23581.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.081956 restraints weight = 14556.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.082902 restraints weight = 10763.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.083436 restraints weight = 8922.791| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22011 Z= 0.193 Angle : 0.621 9.026 29907 Z= 0.325 Chirality : 0.045 0.150 3312 Planarity : 0.004 0.073 3855 Dihedral : 5.097 40.169 3009 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.78 % Allowed : 18.35 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.16), residues: 2724 helix: 1.91 (0.25), residues: 405 sheet: 0.28 (0.18), residues: 888 loop : -0.97 (0.17), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 24 TYR 0.014 0.001 TYR E 102 PHE 0.019 0.002 PHE L 118 TRP 0.009 0.001 TRP I 154 HIS 0.009 0.001 HIS J 198 Details of bonding type rmsd covalent geometry : bond 0.00446 (21990) covalent geometry : angle 0.61750 (29862) SS BOND : bond 0.00365 ( 18) SS BOND : angle 1.74322 ( 36) hydrogen bonds : bond 0.04141 ( 879) hydrogen bonds : angle 4.96013 ( 2493) link_NAG-ASN : bond 0.00177 ( 3) link_NAG-ASN : angle 2.48800 ( 9) *********************** 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 286 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 219 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 477 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8498 (tppt) REVERT: C 293 MET cc_start: 0.8953 (mmt) cc_final: 0.8650 (mmt) REVERT: E 293 MET cc_start: 0.9034 (mmt) cc_final: 0.8588 (mmt) REVERT: F 377 LYS cc_start: 0.8684 (ttmt) cc_final: 0.8116 (ttmm) REVERT: F 439 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7369 (tm-30) REVERT: G 13 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8062 (mtmm) REVERT: H 24 ARG cc_start: 0.8427 (ttm110) cc_final: 0.8126 (ttm110) REVERT: H 138 ASN cc_start: 0.7849 (m-40) cc_final: 0.7470 (t0) REVERT: H 142 ARG cc_start: 0.8588 (ttt-90) cc_final: 0.8192 (mtt-85) REVERT: H 161 GLU cc_start: 0.8930 (pp20) cc_final: 0.8517 (pp20) REVERT: H 189 HIS cc_start: 0.7686 (m-70) cc_final: 0.7124 (m-70) REVERT: I 100 ASN cc_start: 0.8394 (m-40) cc_final: 0.8155 (m-40) REVERT: I 105 GLN cc_start: 0.8768 (pp30) cc_final: 0.7830 (pp30) REVERT: I 145 TYR cc_start: 0.7063 (p90) cc_final: 0.6589 (p90) REVERT: K 32 ASP cc_start: 0.8950 (p0) cc_final: 0.8650 (p0) REVERT: K 105 GLN cc_start: 0.8751 (pp30) cc_final: 0.7954 (pp30) REVERT: K 166 PHE cc_start: 0.7937 (m-80) cc_final: 0.7711 (m-10) REVERT: J 105 GLU cc_start: 0.8014 (tp30) cc_final: 0.7383 (tp30) REVERT: J 161 GLU cc_start: 0.8945 (pp20) cc_final: 0.8371 (pp20) REVERT: L 24 ARG cc_start: 0.8259 (ttm-80) cc_final: 0.7935 (ttm110) REVERT: L 36 TYR cc_start: 0.8948 (m-80) cc_final: 0.8585 (m-10) REVERT: L 138 ASN cc_start: 0.7968 (m110) cc_final: 0.7264 (m-40) REVERT: L 161 GLU cc_start: 0.8726 (pp20) cc_final: 0.8357 (pp20) REVERT: L 170 ASP cc_start: 0.7079 (t0) cc_final: 0.6814 (t0) REVERT: L 195 GLU cc_start: 0.6380 (tm-30) cc_final: 0.6006 (tp30) outliers start: 67 outliers final: 62 residues processed: 276 average time/residue: 0.1770 time to fit residues: 74.6191 Evaluate side-chains 277 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 213 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 109 LEU 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 436 MET 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 142 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 E residue 152 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 278 CYS Chi-restraints excluded: chain F residue 396 GLN Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 482 CYS Chi-restraints excluded: chain G residue 13 LYS 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 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 G residue 198 VAL 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 146 VAL Chi-restraints excluded: chain H residue 163 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 70 ASN 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 165 THR 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 70 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 165 THR 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 85 THR Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain L residue 22 THR 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 268 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 186 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 164 optimal weight: 20.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.103215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.075298 restraints weight = 52077.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.077654 restraints weight = 23710.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.079171 restraints weight = 14696.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.080135 restraints weight = 10881.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.080677 restraints weight = 8986.444| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 22011 Z= 0.203 Angle : 0.633 9.220 29907 Z= 0.331 Chirality : 0.045 0.151 3312 Planarity : 0.004 0.071 3855 Dihedral : 5.134 40.087 3009 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.70 % Allowed : 18.39 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.16), residues: 2724 helix: 1.91 (0.24), residues: 402 sheet: 0.27 (0.18), residues: 888 loop : -0.98 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 24 TYR 0.016 0.001 TYR H 186 PHE 0.018 0.002 PHE H 139 TRP 0.010 0.001 TRP I 154 HIS 0.008 0.001 HIS J 198 Details of bonding type rmsd covalent geometry : bond 0.00471 (21990) covalent geometry : angle 0.62859 (29862) SS BOND : bond 0.00375 ( 18) SS BOND : angle 1.85352 ( 36) hydrogen bonds : bond 0.04189 ( 879) hydrogen bonds : angle 4.99262 ( 2493) link_NAG-ASN : bond 0.00163 ( 3) link_NAG-ASN : angle 2.52832 ( 9) ********************** 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 283 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 218 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 477 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8517 (tppt) REVERT: C 57 ARG cc_start: 0.7811 (ttm110) cc_final: 0.7529 (ttm110) REVERT: C 293 MET cc_start: 0.8942 (mmt) cc_final: 0.8670 (mmt) REVERT: E 293 MET cc_start: 0.9036 (mmt) cc_final: 0.8590 (mmt) REVERT: F 377 LYS cc_start: 0.8687 (ttmt) cc_final: 0.8116 (ttmm) REVERT: F 439 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7223 (tm-30) REVERT: G 13 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7964 (mtmm) REVERT: H 24 ARG cc_start: 0.8435 (ttm110) cc_final: 0.8146 (ttm110) REVERT: H 138 ASN cc_start: 0.7930 (m-40) cc_final: 0.7471 (t0) REVERT: H 142 ARG cc_start: 0.8643 (ttt-90) cc_final: 0.8235 (mtt-85) REVERT: H 161 GLU cc_start: 0.8898 (pp20) cc_final: 0.8518 (pp20) REVERT: H 189 HIS cc_start: 0.7708 (m-70) cc_final: 0.7073 (m-70) REVERT: I 100 ASN cc_start: 0.8408 (m-40) cc_final: 0.8152 (m-40) REVERT: I 105 GLN cc_start: 0.8772 (pp30) cc_final: 0.7824 (pp30) REVERT: I 145 TYR cc_start: 0.7108 (p90) cc_final: 0.6715 (p90) REVERT: K 32 ASP cc_start: 0.8959 (p0) cc_final: 0.8659 (p0) REVERT: K 105 GLN cc_start: 0.8762 (pp30) cc_final: 0.7974 (pp30) REVERT: K 117 LYS cc_start: 0.8356 (mmtt) cc_final: 0.8145 (mmtt) REVERT: K 166 PHE cc_start: 0.7974 (m-80) cc_final: 0.7759 (m-10) REVERT: J 105 GLU cc_start: 0.7969 (tp30) cc_final: 0.7364 (tp30) REVERT: J 138 ASN cc_start: 0.7959 (m110) cc_final: 0.7230 (m-40) REVERT: J 161 GLU cc_start: 0.8873 (pp20) cc_final: 0.8329 (pp20) REVERT: L 24 ARG cc_start: 0.8190 (ttm-80) cc_final: 0.7861 (ttm110) REVERT: L 36 TYR cc_start: 0.8950 (m-80) cc_final: 0.8579 (m-10) REVERT: L 138 ASN cc_start: 0.8026 (m110) cc_final: 0.7373 (m-40) REVERT: L 161 GLU cc_start: 0.8730 (pp20) cc_final: 0.8391 (pp20) REVERT: L 170 ASP cc_start: 0.7026 (t0) cc_final: 0.6764 (t0) REVERT: L 195 GLU cc_start: 0.6345 (tm-30) cc_final: 0.6009 (tp30) outliers start: 65 outliers final: 59 residues processed: 271 average time/residue: 0.1761 time to fit residues: 72.9276 Evaluate side-chains 274 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 213 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 109 LEU 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 436 MET 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 142 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 278 CYS Chi-restraints excluded: chain F residue 396 GLN Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 482 CYS Chi-restraints excluded: chain G residue 13 LYS 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 165 THR Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 163 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 70 ASN 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 165 THR 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 70 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 165 THR Chi-restraints excluded: chain K residue 197 ASN Chi-restraints excluded: chain K residue 198 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain L residue 22 THR 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 208 optimal weight: 0.3980 chunk 84 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 chunk 265 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 259 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 203 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 396 GLN ** 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 = 0.3665 r_free = 0.3665 target = 0.106786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.079106 restraints weight = 51718.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.081493 restraints weight = 23453.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.083026 restraints weight = 14422.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.083956 restraints weight = 10613.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.084582 restraints weight = 8794.239| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4601 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= 0.142 Angle : 0.598 8.878 29907 Z= 0.313 Chirality : 0.044 0.150 3312 Planarity : 0.004 0.073 3855 Dihedral : 4.942 39.234 3009 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.37 % Allowed : 18.80 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.16), residues: 2724 helix: 2.06 (0.25), residues: 402 sheet: 0.20 (0.18), residues: 903 loop : -0.87 (0.17), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 24 TYR 0.021 0.001 TYR C 141 PHE 0.019 0.002 PHE H 139 TRP 0.011 0.001 TRP I 154 HIS 0.009 0.001 HIS J 198 Details of bonding type rmsd covalent geometry : bond 0.00325 (21990) covalent geometry : angle 0.59482 (29862) SS BOND : bond 0.00288 ( 18) SS BOND : angle 1.53664 ( 36) hydrogen bonds : bond 0.03884 ( 879) hydrogen bonds : angle 4.83950 ( 2493) link_NAG-ASN : bond 0.00180 ( 3) link_NAG-ASN : angle 2.46118 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4362.86 seconds wall clock time: 76 minutes 41.90 seconds (4601.90 seconds total)