Starting phenix.real_space_refine on Sun Jun 15 08:51:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tp9_41470/06_2025/8tp9_41470.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tp9_41470/06_2025/8tp9_41470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tp9_41470/06_2025/8tp9_41470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tp9_41470/06_2025/8tp9_41470.map" model { file = "/net/cci-nas-00/data/ceres_data/8tp9_41470/06_2025/8tp9_41470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tp9_41470/06_2025/8tp9_41470.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 10740 2.51 5 N 2934 2.21 5 O 3357 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17118 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3816 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 19, 'TRANS': 461} Chain breaks: 1 Chain: "B" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3816 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 19, 'TRANS': 461} Chain breaks: 1 Chain: "C" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3816 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 19, 'TRANS': 461} Chain breaks: 1 Chain: "D" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "E" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "F" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "L" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 10.51, per 1000 atoms: 0.61 Number of scatterers: 17118 At special positions: 0 Unit cell: (128.8, 129.95, 146.05, 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 87 16.00 O 3357 8.00 N 2934 7.00 C 10740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.04 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.02 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.04 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.02 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.02 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 477 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.04 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.02 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.01 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A 501 " - " ASN A 483 " " NAG A 502 " - " ASN A 33 " " NAG A 503 " - " ASN A 289 " " NAG B 501 " - " ASN B 483 " " NAG B 502 " - " ASN B 33 " " NAG B 503 " - " ASN B 289 " " NAG C 501 " - " ASN C 483 " " NAG C 502 " - " ASN C 33 " " NAG C 503 " - " ASN C 289 " " NAG I 1 " - " ASN A 169 " " NAG J 1 " - " ASN B 169 " " NAG K 1 " - " ASN C 169 " Time building additional restraints: 3.83 Conformation dependent library (CDL) restraints added in 2.0 seconds 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3900 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 51 sheets defined 18.3% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 125 through 127 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 366 through 386 Processing helix chain 'A' and resid 403 through 456 Processing helix chain 'A' and resid 474 through 482 Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 125 through 127 Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 366 through 386 Processing helix chain 'B' and resid 403 through 456 Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 125 through 127 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 366 through 386 Processing helix chain 'C' and resid 403 through 456 Processing helix chain 'C' and resid 474 through 482 Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.328A pdb=" N LEU A 51 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 59 through 62 removed outlier: 6.176A pdb=" N LEU A 59 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.694A pdb=" N SER A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N TRP A 234 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N HIS A 117 " --> pdb=" O SER A 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.694A pdb=" N SER A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N TRP A 234 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.494A pdb=" N ALA A 138 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N ASN A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 168 Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AB3, first strand: chain 'B' and resid 364 through 365 Processing sheet with id=AB4, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AB5, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.328A pdb=" N LEU B 51 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N CYS B 277 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 59 through 62 removed outlier: 6.176A pdb=" N LEU B 59 " --> pdb=" O MET B 88 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.694A pdb=" N SER B 101 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N TRP B 234 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N HIS B 117 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.694A pdb=" N SER B 101 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N TRP B 234 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 136 through 141 removed outlier: 7.493A pdb=" N ALA B 138 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N ASN B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 164 through 168 Processing sheet with id=AC4, first strand: chain 'B' and resid 286 through 287 Processing sheet with id=AC5, first strand: chain 'C' and resid 364 through 365 Processing sheet with id=AC6, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AC7, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC8, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC9, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.328A pdb=" N LEU C 51 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 59 through 62 removed outlier: 6.176A pdb=" N LEU C 59 " --> pdb=" O MET C 88 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.694A pdb=" N SER C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N TRP C 234 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N HIS C 117 " --> pdb=" O SER C 261 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.694A pdb=" N SER C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N TRP C 234 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.493A pdb=" N ALA C 138 " --> pdb=" O ASN C 144 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N ASN C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 164 through 168 Processing sheet with id=AD6, first strand: chain 'C' and resid 286 through 287 Processing sheet with id=AD7, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.585A pdb=" N TYR D 35 " --> pdb=" O GLU D 95 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 11 through 12 removed outlier: 7.079A pdb=" N CYS D 92 " --> pdb=" O TRP D 103 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TRP D 103 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.585A pdb=" N TYR E 35 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.080A pdb=" N CYS E 92 " --> pdb=" O TRP E 103 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TRP E 103 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AE5, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.529A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA F 84 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.529A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA F 84 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.529A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA G 84 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.529A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA G 84 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.585A pdb=" N TYR H 35 " --> pdb=" O GLU H 95 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.079A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.529A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.529A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 717 hydrogen bonds defined for protein. 1863 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: 6.53 Time building geometry restraints manager: 4.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4168 1.32 - 1.46: 5445 1.46 - 1.60: 7741 1.60 - 1.73: 31 1.73 - 1.87: 120 Bond restraints: 17505 Sorted by residual: bond pdb=" CB HIS B 354 " pdb=" CG HIS B 354 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.11e+01 bond pdb=" CB HIS C 354 " pdb=" CG HIS C 354 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.09e+01 bond pdb=" CB HIS A 354 " pdb=" CG HIS A 354 " ideal model delta sigma weight residual 1.497 1.408 0.089 1.40e-02 5.10e+03 4.07e+01 bond pdb=" CG MET B 151 " pdb=" SD MET B 151 " ideal model delta sigma weight residual 1.803 1.684 0.119 2.50e-02 1.60e+03 2.26e+01 bond pdb=" CG MET C 151 " pdb=" SD MET C 151 " ideal model delta sigma weight residual 1.803 1.684 0.119 2.50e-02 1.60e+03 2.25e+01 ... (remaining 17500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.22: 23660 7.22 - 14.44: 58 14.44 - 21.66: 0 21.66 - 28.89: 0 28.89 - 36.11: 3 Bond angle restraints: 23721 Sorted by residual: angle pdb=" C2 NAG J 1 " pdb=" N2 NAG J 1 " pdb=" C7 NAG J 1 " ideal model delta sigma weight residual 124.56 160.67 -36.11 3.00e+00 1.11e-01 1.45e+02 angle pdb=" C2 NAG K 1 " pdb=" N2 NAG K 1 " pdb=" C7 NAG K 1 " ideal model delta sigma weight residual 124.56 160.66 -36.10 3.00e+00 1.11e-01 1.45e+02 angle pdb=" C2 NAG I 1 " pdb=" N2 NAG I 1 " pdb=" C7 NAG I 1 " ideal model delta sigma weight residual 124.56 160.64 -36.08 3.00e+00 1.11e-01 1.45e+02 angle pdb=" N THR C 318 " pdb=" CA THR C 318 " pdb=" C THR C 318 " ideal model delta sigma weight residual 114.56 103.34 11.22 1.27e+00 6.20e-01 7.80e+01 angle pdb=" N THR B 318 " pdb=" CA THR B 318 " pdb=" C THR B 318 " ideal model delta sigma weight residual 114.56 103.37 11.19 1.27e+00 6.20e-01 7.76e+01 ... (remaining 23716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 10196 17.52 - 35.04: 299 35.04 - 52.56: 64 52.56 - 70.09: 61 70.09 - 87.61: 15 Dihedral angle restraints: 10635 sinusoidal: 4503 harmonic: 6132 Sorted by residual: dihedral pdb=" C TRP C 84 " pdb=" N TRP C 84 " pdb=" CA TRP C 84 " pdb=" CB TRP C 84 " ideal model delta harmonic sigma weight residual -122.60 -108.36 -14.24 0 2.50e+00 1.60e-01 3.24e+01 dihedral pdb=" C TRP B 84 " pdb=" N TRP B 84 " pdb=" CA TRP B 84 " pdb=" CB TRP B 84 " ideal model delta harmonic sigma weight residual -122.60 -108.36 -14.24 0 2.50e+00 1.60e-01 3.24e+01 dihedral pdb=" C TRP A 84 " pdb=" N TRP A 84 " pdb=" CA TRP A 84 " pdb=" CB TRP A 84 " ideal model delta harmonic sigma weight residual -122.60 -108.39 -14.21 0 2.50e+00 1.60e-01 3.23e+01 ... (remaining 10632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1764 0.092 - 0.183: 596 0.183 - 0.275: 156 0.275 - 0.367: 49 0.367 - 0.458: 24 Chirality restraints: 2589 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.26e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.25e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.24e+02 ... (remaining 2586 not shown) Planarity restraints: 3069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 84 " 0.102 2.00e-02 2.50e+03 4.84e-02 5.86e+01 pdb=" CG TRP B 84 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 84 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 84 " -0.049 2.00e-02 2.50e+03 pdb=" NE1 TRP B 84 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP B 84 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 84 " -0.054 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 84 " 0.054 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 84 " -0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP B 84 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 84 " -0.102 2.00e-02 2.50e+03 4.84e-02 5.85e+01 pdb=" CG TRP A 84 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A 84 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 84 " 0.049 2.00e-02 2.50e+03 pdb=" NE1 TRP A 84 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP A 84 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 84 " 0.053 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 84 " -0.054 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 84 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP A 84 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 84 " 0.102 2.00e-02 2.50e+03 4.84e-02 5.85e+01 pdb=" CG TRP C 84 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP C 84 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP C 84 " -0.049 2.00e-02 2.50e+03 pdb=" NE1 TRP C 84 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP C 84 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP C 84 " -0.054 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 84 " 0.054 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 84 " -0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP C 84 " 0.044 2.00e-02 2.50e+03 ... (remaining 3066 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 5343 2.85 - 3.36: 15237 3.36 - 3.87: 29165 3.87 - 4.39: 35114 4.39 - 4.90: 57536 Nonbonded interactions: 142395 Sorted by model distance: nonbonded pdb=" O ALA B 336 " pdb=" NE1 TRP B 343 " model vdw 2.334 3.120 nonbonded pdb=" O ALA C 336 " pdb=" NE1 TRP C 343 " model vdw 2.384 3.120 nonbonded pdb=" N THR C 318 " pdb=" N GLY C 319 " model vdw 2.414 2.560 nonbonded pdb=" N THR B 318 " pdb=" N GLY B 319 " model vdw 2.414 2.560 nonbonded pdb=" N THR A 318 " pdb=" N GLY A 319 " model vdw 2.415 2.560 ... (remaining 142390 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 41.780 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 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 : 0.020 0.155 17544 Z= 1.089 Angle : 1.826 36.106 23814 Z= 1.203 Chirality : 0.108 0.458 2589 Planarity : 0.008 0.048 3057 Dihedral : 10.910 87.607 6663 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.17), residues: 2118 helix: 0.41 (0.24), residues: 327 sheet: 0.99 (0.22), residues: 456 loop : 0.33 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.102 0.010 TRP B 84 HIS 0.019 0.003 HIS C 18 PHE 0.036 0.006 PHE C 118 TYR 0.062 0.008 TYR D 50 ARG 0.007 0.001 ARG C 262A Details of bonding type rmsd link_NAG-ASN : bond 0.07409 ( 12) link_NAG-ASN : angle 2.86706 ( 36) link_BETA1-4 : bond 0.07189 ( 3) link_BETA1-4 : angle 5.36445 ( 9) hydrogen bonds : bond 0.12850 ( 663) hydrogen bonds : angle 7.77842 ( 1863) SS BOND : bond 0.00875 ( 24) SS BOND : angle 2.95803 ( 48) covalent geometry : bond 0.02023 (17505) covalent geometry : angle 1.81796 (23721) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.7585 (pt0) cc_final: 0.7262 (pt0) REVERT: A 268 MET cc_start: 0.7967 (ttm) cc_final: 0.7584 (ttm) REVERT: A 456 ARG cc_start: 0.7461 (mtt180) cc_final: 0.6325 (ptt-90) REVERT: B 15 ILE cc_start: 0.8334 (mt) cc_final: 0.8119 (mt) REVERT: B 276 ASN cc_start: 0.8370 (t0) cc_final: 0.7983 (t0) REVERT: B 456 ARG cc_start: 0.7693 (mtt180) cc_final: 0.6281 (ptt-90) REVERT: C 125 LYS cc_start: 0.7445 (pttt) cc_final: 0.7225 (ptpt) REVERT: C 276 ASN cc_start: 0.8157 (t0) cc_final: 0.7752 (t0) REVERT: C 456 ARG cc_start: 0.7410 (mtt180) cc_final: 0.7093 (mtm110) REVERT: D 105 GLN cc_start: 0.6669 (mp10) cc_final: 0.6437 (pm20) REVERT: G 7 SER cc_start: 0.5669 (t) cc_final: 0.5468 (m) REVERT: G 45 LYS cc_start: 0.7486 (tttt) cc_final: 0.7280 (tttp) outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.3259 time to fit residues: 212.0720 Evaluate side-chains 250 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS A 196 GLN A 197 ASN A 410 ASN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS B 197 ASN B 424 ASN B 471 HIS C 197 ASN C 424 ASN C 471 HIS F 27 HIS F 34 ASN F 89 GLN G 27 HIS L 27 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.175806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.148490 restraints weight = 21763.553| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.11 r_work: 0.3672 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17544 Z= 0.184 Angle : 0.715 11.334 23814 Z= 0.379 Chirality : 0.047 0.228 2589 Planarity : 0.004 0.036 3057 Dihedral : 6.254 66.356 2649 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.66 % Allowed : 7.19 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.17), residues: 2118 helix: 1.85 (0.27), residues: 321 sheet: 0.35 (0.21), residues: 558 loop : -0.14 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 84 HIS 0.009 0.001 HIS A 355 PHE 0.021 0.003 PHE C 439 TYR 0.027 0.002 TYR A 105 ARG 0.005 0.000 ARG F 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 12) link_NAG-ASN : angle 2.50329 ( 36) link_BETA1-4 : bond 0.00268 ( 3) link_BETA1-4 : angle 2.64284 ( 9) hydrogen bonds : bond 0.04510 ( 663) hydrogen bonds : angle 6.10766 ( 1863) SS BOND : bond 0.00927 ( 24) SS BOND : angle 1.34747 ( 48) covalent geometry : bond 0.00420 (17505) covalent geometry : angle 0.70571 (23721) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 301 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8119 (pt0) cc_final: 0.7583 (pt0) REVERT: A 53 LYS cc_start: 0.8852 (mtmt) cc_final: 0.8517 (mttp) REVERT: A 147 PHE cc_start: 0.8106 (t80) cc_final: 0.7882 (t80) REVERT: A 268 MET cc_start: 0.8128 (ttm) cc_final: 0.7347 (ttm) REVERT: A 412 LYS cc_start: 0.8448 (tmtt) cc_final: 0.7713 (mtmt) REVERT: A 456 ARG cc_start: 0.7621 (mtt180) cc_final: 0.6740 (mtm110) REVERT: A 460 LYS cc_start: 0.8251 (pttt) cc_final: 0.7729 (ptmm) REVERT: B 147 PHE cc_start: 0.8035 (t80) cc_final: 0.7744 (t80) REVERT: B 176 MET cc_start: 0.8324 (ttm) cc_final: 0.8107 (ttm) REVERT: B 211 LYS cc_start: 0.8067 (tttm) cc_final: 0.7733 (ttmm) REVERT: C 53 LYS cc_start: 0.9049 (mtmt) cc_final: 0.8769 (mttp) REVERT: C 151 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7510 (mmt) REVERT: C 276 ASN cc_start: 0.8709 (t0) cc_final: 0.8341 (t0) REVERT: C 379 ASN cc_start: 0.8240 (m-40) cc_final: 0.7962 (m110) REVERT: C 460 LYS cc_start: 0.8297 (pttt) cc_final: 0.8078 (ptmt) REVERT: D 11 LEU cc_start: 0.8309 (mp) cc_final: 0.8030 (tp) REVERT: D 105 GLN cc_start: 0.7103 (mp10) cc_final: 0.6581 (pm20) REVERT: H 105 GLN cc_start: 0.7471 (mp10) cc_final: 0.6861 (pm20) REVERT: L 61 ARG cc_start: 0.6912 (ptt-90) cc_final: 0.6598 (ptt-90) outliers start: 31 outliers final: 12 residues processed: 316 average time/residue: 0.2951 time to fit residues: 138.9358 Evaluate side-chains 261 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 248 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 121 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 192 optimal weight: 0.5980 chunk 142 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN C 244 ASN ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 ASN D 39 GLN E 39 GLN F 34 ASN F 38 GLN G 38 GLN H 39 GLN L 38 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.173899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.147097 restraints weight = 21764.739| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.06 r_work: 0.3655 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17544 Z= 0.150 Angle : 0.624 11.195 23814 Z= 0.327 Chirality : 0.044 0.215 2589 Planarity : 0.004 0.033 3057 Dihedral : 5.835 62.846 2649 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.09 % Allowed : 9.39 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.17), residues: 2118 helix: 1.79 (0.27), residues: 327 sheet: 0.14 (0.21), residues: 564 loop : -0.16 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 84 HIS 0.008 0.001 HIS A 355 PHE 0.028 0.002 PHE C 147 TYR 0.018 0.002 TYR A 105 ARG 0.004 0.000 ARG G 96 Details of bonding type rmsd link_NAG-ASN : bond 0.00375 ( 12) link_NAG-ASN : angle 2.27343 ( 36) link_BETA1-4 : bond 0.00804 ( 3) link_BETA1-4 : angle 2.39073 ( 9) hydrogen bonds : bond 0.04022 ( 663) hydrogen bonds : angle 5.77829 ( 1863) SS BOND : bond 0.00959 ( 24) SS BOND : angle 1.06628 ( 48) covalent geometry : bond 0.00346 (17505) covalent geometry : angle 0.61568 (23721) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 274 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8179 (pt0) cc_final: 0.7581 (pt0) REVERT: A 147 PHE cc_start: 0.8189 (t80) cc_final: 0.7832 (t80) REVERT: A 412 LYS cc_start: 0.8402 (tmtt) cc_final: 0.7607 (mtmt) REVERT: A 456 ARG cc_start: 0.7600 (mtt180) cc_final: 0.6683 (mtm110) REVERT: B 147 PHE cc_start: 0.8125 (t80) cc_final: 0.7851 (t80) REVERT: B 176 MET cc_start: 0.8349 (ttm) cc_final: 0.8087 (ttm) REVERT: B 211 LYS cc_start: 0.8137 (tttm) cc_final: 0.7829 (ttmm) REVERT: C 53 LYS cc_start: 0.9030 (mtmt) cc_final: 0.8728 (mttp) REVERT: C 114 SER cc_start: 0.7852 (m) cc_final: 0.7534 (p) REVERT: C 151 MET cc_start: 0.8120 (mtt) cc_final: 0.7595 (mmt) REVERT: C 379 ASN cc_start: 0.8233 (m-40) cc_final: 0.7939 (m110) REVERT: C 419 ASP cc_start: 0.8464 (m-30) cc_final: 0.8122 (m-30) REVERT: C 478 MET cc_start: 0.6992 (mmt) cc_final: 0.6524 (mmt) REVERT: D 3 GLN cc_start: 0.8124 (mt0) cc_final: 0.7794 (tt0) REVERT: D 105 GLN cc_start: 0.7161 (mp10) cc_final: 0.6584 (pm20) REVERT: E 46 GLU cc_start: 0.7407 (tt0) cc_final: 0.6415 (pm20) REVERT: F 81 GLU cc_start: 0.5813 (mp0) cc_final: 0.5591 (pt0) REVERT: F 103 ARG cc_start: 0.8452 (ttm110) cc_final: 0.7815 (mtt90) REVERT: G 61 ARG cc_start: 0.6707 (ptp90) cc_final: 0.6217 (ptt-90) REVERT: H 91 TYR cc_start: 0.7824 (m-80) cc_final: 0.7219 (m-80) REVERT: H 105 GLN cc_start: 0.7487 (mp10) cc_final: 0.6934 (pm20) outliers start: 39 outliers final: 25 residues processed: 294 average time/residue: 0.2987 time to fit residues: 131.7001 Evaluate side-chains 257 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 232 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 157 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 32 optimal weight: 0.0980 chunk 164 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 146 optimal weight: 0.3980 chunk 170 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 454 GLN B 454 GLN C 110 HIS C 454 GLN F 34 ASN ** H 35BASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.173500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.146670 restraints weight = 21781.240| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.05 r_work: 0.3649 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17544 Z= 0.126 Angle : 0.583 9.711 23814 Z= 0.302 Chirality : 0.043 0.281 2589 Planarity : 0.004 0.038 3057 Dihedral : 5.605 58.197 2649 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.47 % Allowed : 10.36 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.18), residues: 2118 helix: 1.50 (0.26), residues: 345 sheet: -0.03 (0.21), residues: 564 loop : -0.30 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 84 HIS 0.005 0.001 HIS A 355 PHE 0.016 0.002 PHE F 32 TYR 0.027 0.002 TYR B 105 ARG 0.004 0.000 ARG A 137 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 12) link_NAG-ASN : angle 2.71972 ( 36) link_BETA1-4 : bond 0.00398 ( 3) link_BETA1-4 : angle 2.02390 ( 9) hydrogen bonds : bond 0.03663 ( 663) hydrogen bonds : angle 5.53497 ( 1863) SS BOND : bond 0.00304 ( 24) SS BOND : angle 1.05472 ( 48) covalent geometry : bond 0.00291 (17505) covalent geometry : angle 0.57132 (23721) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 261 time to evaluate : 1.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8213 (pt0) cc_final: 0.7675 (pt0) REVERT: A 147 PHE cc_start: 0.8153 (t80) cc_final: 0.7752 (t80) REVERT: A 304 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7311 (pt0) REVERT: A 412 LYS cc_start: 0.8441 (tmtt) cc_final: 0.7636 (mtmt) REVERT: A 456 ARG cc_start: 0.7923 (mtt180) cc_final: 0.6759 (mtm110) REVERT: B 176 MET cc_start: 0.8376 (ttm) cc_final: 0.8125 (ttm) REVERT: B 211 LYS cc_start: 0.8145 (tttm) cc_final: 0.7834 (ttmm) REVERT: C 53 LYS cc_start: 0.9015 (mtmt) cc_final: 0.8734 (mttp) REVERT: C 151 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7945 (mmt) REVERT: C 419 ASP cc_start: 0.8465 (m-30) cc_final: 0.8123 (m-30) REVERT: D 3 GLN cc_start: 0.8174 (mt0) cc_final: 0.7678 (tt0) REVERT: D 105 GLN cc_start: 0.7351 (mp10) cc_final: 0.6628 (pm20) REVERT: E 46 GLU cc_start: 0.7623 (tt0) cc_final: 0.6436 (pm20) REVERT: F 81 GLU cc_start: 0.5828 (mp0) cc_final: 0.5500 (pt0) REVERT: F 103 ARG cc_start: 0.8441 (ttm110) cc_final: 0.7883 (mtt90) REVERT: G 61 ARG cc_start: 0.6624 (ptp90) cc_final: 0.6099 (ptt-90) REVERT: G 89 GLN cc_start: 0.7253 (tm-30) cc_final: 0.6737 (tm-30) REVERT: H 91 TYR cc_start: 0.7830 (m-80) cc_final: 0.7316 (m-80) REVERT: H 105 GLN cc_start: 0.7465 (mp10) cc_final: 0.6916 (pm20) REVERT: H 108 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8248 (tp) outliers start: 46 outliers final: 26 residues processed: 292 average time/residue: 0.2949 time to fit residues: 130.6004 Evaluate side-chains 261 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 232 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 145 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 200 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 354 HIS ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 ASN C 454 GLN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35BASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.168671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.140576 restraints weight = 22017.959| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.14 r_work: 0.3576 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17544 Z= 0.198 Angle : 0.653 12.390 23814 Z= 0.337 Chirality : 0.045 0.177 2589 Planarity : 0.004 0.034 3057 Dihedral : 5.580 51.140 2649 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.68 % Allowed : 11.59 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.17), residues: 2118 helix: 1.44 (0.26), residues: 345 sheet: -0.35 (0.20), residues: 591 loop : -0.63 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 69 HIS 0.007 0.002 HIS A 184 PHE 0.019 0.002 PHE A 439 TYR 0.022 0.002 TYR C 105 ARG 0.005 0.000 ARG A 137 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 12) link_NAG-ASN : angle 2.39878 ( 36) link_BETA1-4 : bond 0.00470 ( 3) link_BETA1-4 : angle 1.82859 ( 9) hydrogen bonds : bond 0.03850 ( 663) hydrogen bonds : angle 5.71522 ( 1863) SS BOND : bond 0.00494 ( 24) SS BOND : angle 1.49535 ( 48) covalent geometry : bond 0.00472 (17505) covalent geometry : angle 0.64345 (23721) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 247 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.8324 (t80) cc_final: 0.7963 (t80) REVERT: A 268 MET cc_start: 0.8177 (ttm) cc_final: 0.7566 (ttm) REVERT: A 412 LYS cc_start: 0.8482 (tmtt) cc_final: 0.7708 (mtmt) REVERT: A 456 ARG cc_start: 0.7757 (mtt180) cc_final: 0.6830 (mtm110) REVERT: B 84 TRP cc_start: 0.8143 (OUTLIER) cc_final: 0.7389 (m-10) REVERT: B 176 MET cc_start: 0.8528 (ttm) cc_final: 0.8237 (ttm) REVERT: C 53 LYS cc_start: 0.9034 (mtmt) cc_final: 0.8573 (mttp) REVERT: C 151 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8120 (mmt) REVERT: C 419 ASP cc_start: 0.8508 (m-30) cc_final: 0.8256 (m-30) REVERT: D 3 GLN cc_start: 0.8149 (mt0) cc_final: 0.7892 (tt0) REVERT: D 105 GLN cc_start: 0.7420 (mp10) cc_final: 0.6725 (pm20) REVERT: E 46 GLU cc_start: 0.7601 (tt0) cc_final: 0.6375 (pm20) REVERT: F 103 ARG cc_start: 0.8511 (ttm110) cc_final: 0.8022 (mtt90) REVERT: G 61 ARG cc_start: 0.6562 (ptp90) cc_final: 0.5965 (ptt180) REVERT: G 82 ASP cc_start: 0.7793 (m-30) cc_final: 0.7187 (m-30) REVERT: H 105 GLN cc_start: 0.7531 (mp10) cc_final: 0.6919 (pm20) REVERT: L 61 ARG cc_start: 0.6993 (ptt-90) cc_final: 0.6712 (ptt-90) REVERT: L 103 ARG cc_start: 0.8179 (ttm110) cc_final: 0.7821 (mtt90) outliers start: 50 outliers final: 32 residues processed: 279 average time/residue: 0.2988 time to fit residues: 124.7420 Evaluate side-chains 257 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 114 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 203 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 128 optimal weight: 0.0970 chunk 75 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.170244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.142365 restraints weight = 21922.054| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.14 r_work: 0.3594 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17544 Z= 0.142 Angle : 0.606 14.451 23814 Z= 0.309 Chirality : 0.043 0.221 2589 Planarity : 0.004 0.032 3057 Dihedral : 5.383 45.302 2649 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.42 % Allowed : 12.24 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.17), residues: 2118 helix: 1.59 (0.27), residues: 345 sheet: -0.35 (0.21), residues: 561 loop : -0.70 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 47 HIS 0.007 0.001 HIS C 18 PHE 0.015 0.002 PHE C 439 TYR 0.026 0.002 TYR B 105 ARG 0.005 0.000 ARG B 137 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 12) link_NAG-ASN : angle 2.23036 ( 36) link_BETA1-4 : bond 0.00368 ( 3) link_BETA1-4 : angle 1.74657 ( 9) hydrogen bonds : bond 0.03657 ( 663) hydrogen bonds : angle 5.58417 ( 1863) SS BOND : bond 0.00347 ( 24) SS BOND : angle 1.42726 ( 48) covalent geometry : bond 0.00334 (17505) covalent geometry : angle 0.59644 (23721) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 237 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.8367 (t80) cc_final: 0.8062 (t80) REVERT: A 268 MET cc_start: 0.8138 (ttm) cc_final: 0.7503 (ttm) REVERT: A 412 LYS cc_start: 0.8463 (tmtt) cc_final: 0.7505 (mtpp) REVERT: A 456 ARG cc_start: 0.7646 (mtt180) cc_final: 0.6780 (mtm110) REVERT: B 84 TRP cc_start: 0.8008 (OUTLIER) cc_final: 0.7346 (m-10) REVERT: B 176 MET cc_start: 0.8485 (ttm) cc_final: 0.8094 (ttm) REVERT: B 478 MET cc_start: 0.7377 (mmm) cc_final: 0.6996 (mmt) REVERT: C 88 MET cc_start: 0.8323 (ttp) cc_final: 0.8084 (ttp) REVERT: C 151 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.8085 (mmt) REVERT: C 419 ASP cc_start: 0.8456 (m-30) cc_final: 0.8165 (m-30) REVERT: D 105 GLN cc_start: 0.7423 (mp10) cc_final: 0.6716 (pm20) REVERT: E 46 GLU cc_start: 0.7594 (tt0) cc_final: 0.6348 (pm20) REVERT: F 103 ARG cc_start: 0.8448 (ttm110) cc_final: 0.7990 (mtt90) REVERT: G 61 ARG cc_start: 0.6549 (ptp90) cc_final: 0.6013 (ptt-90) REVERT: G 82 ASP cc_start: 0.7688 (m-30) cc_final: 0.7138 (m-30) REVERT: H 105 GLN cc_start: 0.7603 (mp10) cc_final: 0.6983 (pm20) REVERT: L 61 ARG cc_start: 0.6972 (ptt-90) cc_final: 0.6704 (ptt-90) REVERT: L 103 ARG cc_start: 0.8130 (ttm110) cc_final: 0.7802 (mtt90) outliers start: 45 outliers final: 31 residues processed: 265 average time/residue: 0.3067 time to fit residues: 121.3707 Evaluate side-chains 251 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 218 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 103 ARG Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 0.8980 chunk 67 optimal weight: 0.0870 chunk 64 optimal weight: 0.9990 chunk 61 optimal weight: 0.0980 chunk 181 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 184 optimal weight: 7.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.170465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.142273 restraints weight = 21743.819| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.17 r_work: 0.3591 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17544 Z= 0.125 Angle : 0.583 16.011 23814 Z= 0.299 Chirality : 0.043 0.186 2589 Planarity : 0.004 0.035 3057 Dihedral : 5.154 37.933 2649 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.47 % Allowed : 12.08 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.17), residues: 2118 helix: 1.71 (0.27), residues: 345 sheet: -0.30 (0.22), residues: 558 loop : -0.72 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 47 HIS 0.006 0.001 HIS C 18 PHE 0.014 0.001 PHE C 439 TYR 0.025 0.001 TYR A 105 ARG 0.005 0.000 ARG C 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 12) link_NAG-ASN : angle 2.01309 ( 36) link_BETA1-4 : bond 0.00326 ( 3) link_BETA1-4 : angle 1.65722 ( 9) hydrogen bonds : bond 0.03527 ( 663) hydrogen bonds : angle 5.45948 ( 1863) SS BOND : bond 0.00287 ( 24) SS BOND : angle 1.28498 ( 48) covalent geometry : bond 0.00293 (17505) covalent geometry : angle 0.57469 (23721) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 238 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.8213 (t80) cc_final: 0.8001 (t80) REVERT: A 268 MET cc_start: 0.8111 (ttm) cc_final: 0.7448 (ttm) REVERT: A 374 PHE cc_start: 0.8605 (t80) cc_final: 0.8372 (t80) REVERT: A 412 LYS cc_start: 0.8387 (tmtt) cc_final: 0.7452 (mtpp) REVERT: A 456 ARG cc_start: 0.7622 (mtt180) cc_final: 0.6786 (mtm110) REVERT: B 84 TRP cc_start: 0.7905 (OUTLIER) cc_final: 0.7077 (m-10) REVERT: B 176 MET cc_start: 0.8460 (ttm) cc_final: 0.8137 (ttm) REVERT: B 478 MET cc_start: 0.7354 (mmm) cc_final: 0.6939 (mmt) REVERT: C 419 ASP cc_start: 0.8447 (m-30) cc_final: 0.8150 (m-30) REVERT: D 105 GLN cc_start: 0.7448 (mp10) cc_final: 0.6816 (pm20) REVERT: E 46 GLU cc_start: 0.7527 (tt0) cc_final: 0.6286 (pm20) REVERT: E 76 ASN cc_start: 0.7067 (m-40) cc_final: 0.6723 (m-40) REVERT: F 103 ARG cc_start: 0.8464 (ttm110) cc_final: 0.8072 (mtt90) REVERT: G 61 ARG cc_start: 0.6572 (ptp90) cc_final: 0.6031 (ptt-90) REVERT: G 82 ASP cc_start: 0.7802 (m-30) cc_final: 0.7222 (m-30) REVERT: H 105 GLN cc_start: 0.7638 (mp10) cc_final: 0.6988 (pm20) REVERT: L 61 ARG cc_start: 0.6915 (ptt-90) cc_final: 0.6656 (ptt-90) REVERT: L 103 ARG cc_start: 0.8172 (ttm110) cc_final: 0.7909 (mtt90) outliers start: 46 outliers final: 35 residues processed: 267 average time/residue: 0.2987 time to fit residues: 120.2121 Evaluate side-chains 258 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 222 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 103 ARG Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 14 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 147 optimal weight: 0.2980 chunk 29 optimal weight: 0.0170 chunk 18 optimal weight: 0.6980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.171248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.143155 restraints weight = 21535.047| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.15 r_work: 0.3600 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17544 Z= 0.120 Angle : 0.587 18.866 23814 Z= 0.297 Chirality : 0.043 0.188 2589 Planarity : 0.004 0.037 3057 Dihedral : 5.017 33.573 2649 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.09 % Allowed : 12.61 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.18), residues: 2118 helix: 1.84 (0.27), residues: 345 sheet: -0.24 (0.22), residues: 558 loop : -0.72 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 47 HIS 0.005 0.001 HIS C 18 PHE 0.017 0.001 PHE B 147 TYR 0.027 0.001 TYR B 105 ARG 0.004 0.000 ARG C 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 12) link_NAG-ASN : angle 1.99145 ( 36) link_BETA1-4 : bond 0.00284 ( 3) link_BETA1-4 : angle 1.60233 ( 9) hydrogen bonds : bond 0.03500 ( 663) hydrogen bonds : angle 5.40353 ( 1863) SS BOND : bond 0.00283 ( 24) SS BOND : angle 1.19381 ( 48) covalent geometry : bond 0.00280 (17505) covalent geometry : angle 0.57930 (23721) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 228 time to evaluate : 1.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.8220 (t80) cc_final: 0.8005 (t80) REVERT: A 167 SER cc_start: 0.8683 (p) cc_final: 0.8462 (t) REVERT: A 268 MET cc_start: 0.8149 (ttm) cc_final: 0.7517 (ttm) REVERT: A 374 PHE cc_start: 0.8583 (t80) cc_final: 0.8353 (t80) REVERT: A 412 LYS cc_start: 0.8408 (tmtt) cc_final: 0.7456 (mtpp) REVERT: A 456 ARG cc_start: 0.7786 (mtt180) cc_final: 0.6895 (mtm110) REVERT: B 84 TRP cc_start: 0.7884 (OUTLIER) cc_final: 0.7057 (m-10) REVERT: B 176 MET cc_start: 0.8439 (ttm) cc_final: 0.8120 (ttm) REVERT: B 478 MET cc_start: 0.7302 (mmm) cc_final: 0.6889 (mmt) REVERT: C 419 ASP cc_start: 0.8458 (m-30) cc_final: 0.8155 (m-30) REVERT: D 105 GLN cc_start: 0.7461 (mp10) cc_final: 0.6823 (pm20) REVERT: E 46 GLU cc_start: 0.7543 (tt0) cc_final: 0.6309 (pm20) REVERT: E 76 ASN cc_start: 0.7033 (m-40) cc_final: 0.6710 (m-40) REVERT: F 103 ARG cc_start: 0.8434 (ttm110) cc_final: 0.8068 (mtt90) REVERT: G 61 ARG cc_start: 0.6578 (ptp90) cc_final: 0.6036 (ptt-90) REVERT: G 82 ASP cc_start: 0.7835 (m-30) cc_final: 0.7244 (m-30) REVERT: H 105 GLN cc_start: 0.7612 (mp10) cc_final: 0.6977 (pm20) REVERT: L 61 ARG cc_start: 0.6892 (ptt-90) cc_final: 0.6642 (ptt-90) outliers start: 39 outliers final: 32 residues processed: 257 average time/residue: 0.3046 time to fit residues: 118.1269 Evaluate side-chains 252 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 219 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 103 ARG Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 62 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.170374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.143334 restraints weight = 21965.995| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.00 r_work: 0.3607 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17544 Z= 0.199 Angle : 0.648 16.414 23814 Z= 0.329 Chirality : 0.045 0.201 2589 Planarity : 0.004 0.036 3057 Dihedral : 5.225 33.943 2649 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.31 % Allowed : 12.45 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.18), residues: 2118 helix: 1.55 (0.27), residues: 351 sheet: -0.42 (0.22), residues: 558 loop : -0.85 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 69 HIS 0.007 0.001 HIS C 18 PHE 0.016 0.002 PHE B 439 TYR 0.023 0.002 TYR B 105 ARG 0.005 0.001 ARG A 435 Details of bonding type rmsd link_NAG-ASN : bond 0.00290 ( 12) link_NAG-ASN : angle 2.08349 ( 36) link_BETA1-4 : bond 0.00343 ( 3) link_BETA1-4 : angle 1.51213 ( 9) hydrogen bonds : bond 0.03704 ( 663) hydrogen bonds : angle 5.59922 ( 1863) SS BOND : bond 0.00467 ( 24) SS BOND : angle 1.28681 ( 48) covalent geometry : bond 0.00479 (17505) covalent geometry : angle 0.64127 (23721) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 221 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 MET cc_start: 0.8105 (ttm) cc_final: 0.7442 (ttm) REVERT: A 374 PHE cc_start: 0.8649 (t80) cc_final: 0.8402 (t80) REVERT: A 412 LYS cc_start: 0.8468 (tmtt) cc_final: 0.7743 (mtmt) REVERT: A 456 ARG cc_start: 0.7598 (mtt180) cc_final: 0.6852 (mtm110) REVERT: B 84 TRP cc_start: 0.8111 (OUTLIER) cc_final: 0.7353 (m-10) REVERT: B 176 MET cc_start: 0.8487 (ttm) cc_final: 0.8021 (ttm) REVERT: C 419 ASP cc_start: 0.8498 (m-30) cc_final: 0.8198 (m-30) REVERT: D 105 GLN cc_start: 0.7532 (mp10) cc_final: 0.6850 (pm20) REVERT: E 46 GLU cc_start: 0.7540 (tt0) cc_final: 0.6259 (pm20) REVERT: E 76 ASN cc_start: 0.7141 (m-40) cc_final: 0.6895 (m-40) REVERT: F 103 ARG cc_start: 0.8512 (ttm110) cc_final: 0.8096 (mtt90) REVERT: G 61 ARG cc_start: 0.6631 (ptp90) cc_final: 0.6023 (ptt180) REVERT: G 103 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7919 (mtt90) REVERT: H 105 GLN cc_start: 0.7637 (mp10) cc_final: 0.6993 (pm20) REVERT: L 61 ARG cc_start: 0.6910 (ptt-90) cc_final: 0.6640 (ptt-90) REVERT: L 103 ARG cc_start: 0.8268 (ttm110) cc_final: 0.7975 (mtt90) outliers start: 43 outliers final: 32 residues processed: 252 average time/residue: 0.3251 time to fit residues: 123.1215 Evaluate side-chains 249 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 2.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 103 ARG Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 58 optimal weight: 0.5980 chunk 207 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.172966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.145636 restraints weight = 21796.401| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.02 r_work: 0.3626 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17544 Z= 0.145 Angle : 0.606 12.812 23814 Z= 0.308 Chirality : 0.043 0.198 2589 Planarity : 0.004 0.038 3057 Dihedral : 5.180 34.705 2649 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.88 % Allowed : 13.04 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.18), residues: 2118 helix: 1.58 (0.27), residues: 351 sheet: -0.34 (0.22), residues: 534 loop : -0.82 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 47 HIS 0.006 0.001 HIS C 18 PHE 0.034 0.002 PHE A 147 TYR 0.024 0.002 TYR C 105 ARG 0.004 0.000 ARG A 435 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 12) link_NAG-ASN : angle 1.97923 ( 36) link_BETA1-4 : bond 0.00282 ( 3) link_BETA1-4 : angle 1.49022 ( 9) hydrogen bonds : bond 0.03549 ( 663) hydrogen bonds : angle 5.52872 ( 1863) SS BOND : bond 0.00337 ( 24) SS BOND : angle 1.22521 ( 48) covalent geometry : bond 0.00347 (17505) covalent geometry : angle 0.59936 (23721) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 232 time to evaluate : 2.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 MET cc_start: 0.8081 (ttm) cc_final: 0.7417 (ttm) REVERT: A 374 PHE cc_start: 0.8631 (t80) cc_final: 0.8394 (t80) REVERT: A 412 LYS cc_start: 0.8457 (tmtt) cc_final: 0.7702 (mtmt) REVERT: A 456 ARG cc_start: 0.7491 (mtt180) cc_final: 0.6770 (mtm110) REVERT: B 84 TRP cc_start: 0.8023 (OUTLIER) cc_final: 0.7236 (m-10) REVERT: B 176 MET cc_start: 0.8458 (ttm) cc_final: 0.8135 (ttm) REVERT: B 321 ARG cc_start: 0.8022 (ttm110) cc_final: 0.7539 (ptp-110) REVERT: B 404 ARG cc_start: 0.8510 (mmm160) cc_final: 0.7856 (mtt-85) REVERT: B 478 MET cc_start: 0.7209 (mmm) cc_final: 0.6380 (mmt) REVERT: C 379 ASN cc_start: 0.8498 (m-40) cc_final: 0.8215 (m110) REVERT: C 419 ASP cc_start: 0.8486 (m-30) cc_final: 0.8185 (m-30) REVERT: D 3 GLN cc_start: 0.8166 (mt0) cc_final: 0.7915 (tt0) REVERT: E 46 GLU cc_start: 0.7545 (tt0) cc_final: 0.6225 (pm20) REVERT: E 76 ASN cc_start: 0.7116 (m-40) cc_final: 0.6885 (m-40) REVERT: F 103 ARG cc_start: 0.8498 (ttm110) cc_final: 0.8100 (mtt90) REVERT: G 61 ARG cc_start: 0.6558 (ptp90) cc_final: 0.5955 (ptt180) REVERT: G 103 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7914 (mtt90) REVERT: H 105 GLN cc_start: 0.7636 (mp10) cc_final: 0.6997 (pm20) REVERT: L 61 ARG cc_start: 0.6890 (ptt-90) cc_final: 0.6635 (ptt-90) REVERT: L 103 ARG cc_start: 0.8205 (ttm110) cc_final: 0.7960 (mtt90) outliers start: 35 outliers final: 30 residues processed: 256 average time/residue: 0.3935 time to fit residues: 150.4049 Evaluate side-chains 257 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 2.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 103 ARG Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 156 optimal weight: 0.1980 chunk 177 optimal weight: 3.9990 chunk 198 optimal weight: 0.0270 chunk 54 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 113 optimal weight: 0.5980 chunk 151 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN C 471 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.173802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.146916 restraints weight = 21658.201| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.99 r_work: 0.3685 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17544 Z= 0.115 Angle : 0.575 12.922 23814 Z= 0.293 Chirality : 0.043 0.191 2589 Planarity : 0.004 0.038 3057 Dihedral : 4.954 33.044 2649 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.88 % Allowed : 12.88 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.18), residues: 2118 helix: 1.67 (0.27), residues: 351 sheet: -0.22 (0.23), residues: 534 loop : -0.78 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 47 HIS 0.005 0.001 HIS C 18 PHE 0.024 0.002 PHE A 147 TYR 0.024 0.001 TYR C 105 ARG 0.005 0.000 ARG F 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00234 ( 12) link_NAG-ASN : angle 1.86442 ( 36) link_BETA1-4 : bond 0.00305 ( 3) link_BETA1-4 : angle 1.52521 ( 9) hydrogen bonds : bond 0.03431 ( 663) hydrogen bonds : angle 5.41873 ( 1863) SS BOND : bond 0.00298 ( 24) SS BOND : angle 1.25411 ( 48) covalent geometry : bond 0.00269 (17505) covalent geometry : angle 0.56833 (23721) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9809.15 seconds wall clock time: 169 minutes 50.86 seconds (10190.86 seconds total)