Starting phenix.real_space_refine on Sun Aug 24 05:01:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tp9_41470/08_2025/8tp9_41470.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tp9_41470/08_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_41470/08_2025/8tp9_41470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tp9_41470/08_2025/8tp9_41470.map" model { file = "/net/cci-nas-00/data/ceres_data/8tp9_41470/08_2025/8tp9_41470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tp9_41470/08_2025/8tp9_41470.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.38, per 1000 atoms: 0.20 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: 1.49 Conformation dependent library (CDL) restraints added in 707.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.79 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: 3.47 Time building geometry restraints manager: 1.96 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: 0.03 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: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.930 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.280 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (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 ARG 0.007 0.001 ARG C 262A TYR 0.062 0.008 TYR D 50 PHE 0.036 0.006 PHE C 118 TRP 0.102 0.010 TRP B 84 HIS 0.019 0.003 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.02023 (17505) covalent geometry : angle 1.81796 (23721) SS BOND : bond 0.00875 ( 24) SS BOND : angle 2.95803 ( 48) hydrogen bonds : bond 0.12850 ( 663) hydrogen bonds : angle 7.77842 ( 1863) link_BETA1-4 : bond 0.07189 ( 3) link_BETA1-4 : angle 5.36445 ( 9) link_NAG-ASN : bond 0.07409 ( 12) link_NAG-ASN : angle 2.86706 ( 36) *********************** 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 : 0.670 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: 0.1467 time to fit residues: 95.4326 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 : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.0470 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 110 HIS A 196 GLN A 197 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 = 0.4101 r_free = 0.4101 target = 0.176692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.149449 restraints weight = 21763.739| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.12 r_work: 0.3682 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17544 Z= 0.172 Angle : 0.710 11.333 23814 Z= 0.377 Chirality : 0.047 0.230 2589 Planarity : 0.004 0.042 3057 Dihedral : 6.237 66.363 2649 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.56 % Allowed : 7.25 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.17), residues: 2118 helix: 1.88 (0.27), residues: 321 sheet: 0.41 (0.21), residues: 558 loop : -0.10 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 61 TYR 0.025 0.002 TYR A 105 PHE 0.020 0.002 PHE C 118 TRP 0.024 0.002 TRP B 84 HIS 0.010 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00391 (17505) covalent geometry : angle 0.70007 (23721) SS BOND : bond 0.00361 ( 24) SS BOND : angle 1.24432 ( 48) hydrogen bonds : bond 0.04562 ( 663) hydrogen bonds : angle 6.09501 ( 1863) link_BETA1-4 : bond 0.00278 ( 3) link_BETA1-4 : angle 2.91846 ( 9) link_NAG-ASN : bond 0.00414 ( 12) link_NAG-ASN : angle 2.52812 ( 36) *********************** 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 334 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 305 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8105 (pt0) cc_final: 0.7572 (pt0) REVERT: A 53 LYS cc_start: 0.8830 (mtmt) cc_final: 0.8502 (mttp) REVERT: A 114 SER cc_start: 0.7855 (m) cc_final: 0.7601 (p) REVERT: A 147 PHE cc_start: 0.8085 (t80) cc_final: 0.7550 (t80) REVERT: A 268 MET cc_start: 0.8125 (ttm) cc_final: 0.7365 (ttm) REVERT: A 412 LYS cc_start: 0.8425 (tmtt) cc_final: 0.7698 (mtmt) REVERT: A 456 ARG cc_start: 0.7604 (mtt180) cc_final: 0.6737 (mtm110) REVERT: A 460 LYS cc_start: 0.8243 (pttt) cc_final: 0.7721 (ptmm) REVERT: B 147 PHE cc_start: 0.8012 (t80) cc_final: 0.7750 (t80) REVERT: B 176 MET cc_start: 0.8286 (ttm) cc_final: 0.8057 (ttm) REVERT: B 211 LYS cc_start: 0.8061 (tttm) cc_final: 0.7725 (ttmm) REVERT: B 460 LYS cc_start: 0.8546 (pttt) cc_final: 0.7950 (ptmm) REVERT: C 53 LYS cc_start: 0.9033 (mtmt) cc_final: 0.8749 (mttp) REVERT: C 151 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7595 (mmt) REVERT: C 379 ASN cc_start: 0.8228 (m-40) cc_final: 0.7951 (m110) REVERT: C 460 LYS cc_start: 0.8297 (pttt) cc_final: 0.8076 (ptmt) REVERT: D 11 LEU cc_start: 0.8336 (mp) cc_final: 0.8002 (tp) REVERT: D 105 GLN cc_start: 0.7081 (mp10) cc_final: 0.6525 (pm20) REVERT: G 61 ARG cc_start: 0.6728 (ptt-90) cc_final: 0.6223 (ptt-90) REVERT: G 89 GLN cc_start: 0.7660 (tt0) cc_final: 0.7261 (tt0) REVERT: H 46 GLU cc_start: 0.6963 (pm20) cc_final: 0.6715 (tt0) REVERT: H 105 GLN cc_start: 0.7443 (mp10) cc_final: 0.6849 (pm20) REVERT: L 61 ARG cc_start: 0.6887 (ptt-90) cc_final: 0.6519 (ptt-90) outliers start: 29 outliers final: 12 residues processed: 320 average time/residue: 0.1371 time to fit residues: 65.7485 Evaluate side-chains 257 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 244 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 88 MET 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 29 ILE 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 L residue 60 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 5.9990 chunk 202 optimal weight: 0.0170 chunk 43 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 overall best weight: 0.8620 ------------------------------------------------------------------------------- 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** B 410 ASN C 244 ASN ** 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 35BASN 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 = 0.4059 r_free = 0.4059 target = 0.172982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.146106 restraints weight = 22050.885| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.07 r_work: 0.3641 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17544 Z= 0.163 Angle : 0.640 12.588 23814 Z= 0.335 Chirality : 0.044 0.224 2589 Planarity : 0.004 0.033 3057 Dihedral : 5.838 62.570 2649 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.25 % Allowed : 9.50 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.17), residues: 2118 helix: 1.78 (0.26), residues: 327 sheet: 0.20 (0.21), residues: 534 loop : -0.22 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 103 TYR 0.021 0.002 TYR A 353 PHE 0.031 0.002 PHE C 147 TRP 0.016 0.002 TRP C 84 HIS 0.008 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00378 (17505) covalent geometry : angle 0.63119 (23721) SS BOND : bond 0.00525 ( 24) SS BOND : angle 1.13830 ( 48) hydrogen bonds : bond 0.04047 ( 663) hydrogen bonds : angle 5.79087 ( 1863) link_BETA1-4 : bond 0.00483 ( 3) link_BETA1-4 : angle 2.27565 ( 9) link_NAG-ASN : bond 0.00371 ( 12) link_NAG-ASN : angle 2.24605 ( 36) *********************** 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 315 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 273 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8151 (pt0) cc_final: 0.7569 (pt0) REVERT: A 147 PHE cc_start: 0.8219 (t80) cc_final: 0.7839 (t80) REVERT: A 412 LYS cc_start: 0.8414 (tmtt) cc_final: 0.7623 (mtmt) REVERT: A 456 ARG cc_start: 0.7749 (mtt180) cc_final: 0.6775 (mtm110) REVERT: B 147 PHE cc_start: 0.8140 (t80) cc_final: 0.7899 (t80) REVERT: B 176 MET cc_start: 0.8407 (ttm) cc_final: 0.8135 (ttm) REVERT: B 211 LYS cc_start: 0.8139 (tttm) cc_final: 0.7839 (ttmm) REVERT: C 53 LYS cc_start: 0.9034 (mtmt) cc_final: 0.8728 (mttp) REVERT: C 114 SER cc_start: 0.7852 (m) cc_final: 0.7652 (p) REVERT: C 151 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7636 (mmt) REVERT: C 276 ASN cc_start: 0.8632 (t0) cc_final: 0.8389 (t0) REVERT: C 379 ASN cc_start: 0.8287 (m-40) cc_final: 0.7945 (m-40) REVERT: C 419 ASP cc_start: 0.8460 (m-30) cc_final: 0.8120 (m-30) REVERT: C 478 MET cc_start: 0.7002 (mmt) cc_final: 0.6505 (mmt) REVERT: D 105 GLN cc_start: 0.7342 (mp10) cc_final: 0.6627 (pm20) REVERT: E 46 GLU cc_start: 0.7642 (tt0) cc_final: 0.6469 (pm20) REVERT: F 81 GLU cc_start: 0.5844 (mp0) cc_final: 0.5642 (pt0) REVERT: H 46 GLU cc_start: 0.7057 (pm20) cc_final: 0.6819 (tt0) REVERT: H 91 TYR cc_start: 0.7787 (m-80) cc_final: 0.7210 (m-80) REVERT: H 105 GLN cc_start: 0.7505 (mp10) cc_final: 0.6939 (pm20) REVERT: L 89 GLN cc_start: 0.7217 (tt0) cc_final: 0.6809 (tt0) outliers start: 42 outliers final: 28 residues processed: 294 average time/residue: 0.1215 time to fit residues: 53.9890 Evaluate side-chains 258 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 229 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 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 151 MET Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain D residue 98 VAL 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 35 ASN 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 123 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 chunk 205 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 198 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 454 GLN C 110 HIS C 454 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.172450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.144835 restraints weight = 22005.419| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.14 r_work: 0.3617 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3443 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= 0.149 Angle : 0.613 12.233 23814 Z= 0.316 Chirality : 0.044 0.301 2589 Planarity : 0.004 0.037 3057 Dihedral : 5.711 58.505 2649 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.63 % Allowed : 10.52 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.17), residues: 2118 helix: 1.48 (0.26), residues: 345 sheet: -0.11 (0.21), residues: 570 loop : -0.34 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 96 TYR 0.024 0.002 TYR B 105 PHE 0.017 0.002 PHE A 439 TRP 0.013 0.002 TRP C 84 HIS 0.006 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00348 (17505) covalent geometry : angle 0.59665 (23721) SS BOND : bond 0.00369 ( 24) SS BOND : angle 1.52902 ( 48) hydrogen bonds : bond 0.03829 ( 663) hydrogen bonds : angle 5.68328 ( 1863) link_BETA1-4 : bond 0.00479 ( 3) link_BETA1-4 : angle 2.09424 ( 9) link_NAG-ASN : bond 0.00278 ( 12) link_NAG-ASN : angle 3.18631 ( 36) *********************** 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 305 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 256 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8227 (pt0) cc_final: 0.7704 (pt0) REVERT: A 147 PHE cc_start: 0.8201 (t80) cc_final: 0.7706 (t80) REVERT: A 304 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7347 (pt0) REVERT: A 412 LYS cc_start: 0.8374 (tmtt) cc_final: 0.7607 (mtmt) REVERT: A 456 ARG cc_start: 0.7940 (mtt180) cc_final: 0.6778 (mtm110) REVERT: B 176 MET cc_start: 0.8446 (ttm) cc_final: 0.8174 (ttm) REVERT: B 211 LYS cc_start: 0.8172 (tttm) cc_final: 0.7862 (ttmm) REVERT: C 53 LYS cc_start: 0.8960 (mtmt) cc_final: 0.8609 (mttp) REVERT: C 151 MET cc_start: 0.8212 (mtt) cc_final: 0.7673 (mmt) REVERT: C 379 ASN cc_start: 0.8340 (m-40) cc_final: 0.8014 (m-40) REVERT: C 419 ASP cc_start: 0.8490 (m-30) cc_final: 0.8147 (m-30) REVERT: D 3 GLN cc_start: 0.8191 (mt0) cc_final: 0.7922 (tt0) REVERT: D 105 GLN cc_start: 0.7369 (mp10) cc_final: 0.6646 (pm20) REVERT: E 46 GLU cc_start: 0.7633 (tt0) cc_final: 0.6435 (pm20) REVERT: F 81 GLU cc_start: 0.5883 (mp0) cc_final: 0.5558 (pt0) REVERT: F 103 ARG cc_start: 0.8500 (ttm110) cc_final: 0.7968 (mtt90) REVERT: G 61 ARG cc_start: 0.6821 (ptt-90) cc_final: 0.6463 (ptt-90) REVERT: H 105 GLN cc_start: 0.7482 (mp10) cc_final: 0.6901 (pm20) REVERT: L 103 ARG cc_start: 0.8152 (ttm110) cc_final: 0.7796 (mtt90) outliers start: 49 outliers final: 30 residues processed: 288 average time/residue: 0.1341 time to fit residues: 58.0142 Evaluate side-chains 257 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 226 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 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 46 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 197 ASN Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 290 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 198 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 37 ILE 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 L residue 60 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 chunk 156 optimal weight: 0.3980 chunk 126 optimal weight: 0.5980 chunk 8 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 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 B 479 ASN C 276 ASN ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.172459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.144691 restraints weight = 21877.556| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.14 r_work: 0.3619 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3677 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= 0.135 Angle : 0.588 10.863 23814 Z= 0.303 Chirality : 0.043 0.179 2589 Planarity : 0.004 0.034 3057 Dihedral : 5.502 54.226 2649 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.63 % Allowed : 11.33 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.18), residues: 2118 helix: 1.58 (0.27), residues: 345 sheet: -0.05 (0.21), residues: 561 loop : -0.48 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 103 TYR 0.024 0.002 TYR C 105 PHE 0.016 0.002 PHE C 439 TRP 0.016 0.001 TRP B 153 HIS 0.005 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00317 (17505) covalent geometry : angle 0.57634 (23721) SS BOND : bond 0.00329 ( 24) SS BOND : angle 1.52064 ( 48) hydrogen bonds : bond 0.03662 ( 663) hydrogen bonds : angle 5.57445 ( 1863) link_BETA1-4 : bond 0.00351 ( 3) link_BETA1-4 : angle 1.89691 ( 9) link_NAG-ASN : bond 0.00310 ( 12) link_NAG-ASN : angle 2.38809 ( 36) *********************** 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 285 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 236 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8263 (pt0) cc_final: 0.7741 (pt0) REVERT: A 147 PHE cc_start: 0.8252 (t80) cc_final: 0.7983 (t80) REVERT: A 412 LYS cc_start: 0.8450 (tmtt) cc_final: 0.7654 (mtmt) REVERT: A 456 ARG cc_start: 0.7913 (mtt180) cc_final: 0.6771 (mtm110) REVERT: B 176 MET cc_start: 0.8436 (ttm) cc_final: 0.8154 (ttm) REVERT: B 478 MET cc_start: 0.7327 (mmm) cc_final: 0.6937 (mmt) REVERT: C 151 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7961 (mmt) REVERT: C 379 ASN cc_start: 0.8373 (m-40) cc_final: 0.8066 (m110) REVERT: C 419 ASP cc_start: 0.8479 (m-30) cc_final: 0.8207 (m-30) REVERT: C 478 MET cc_start: 0.6630 (mmt) cc_final: 0.6045 (mmt) REVERT: C 482 LYS cc_start: 0.7549 (mtmm) cc_final: 0.7269 (mptt) REVERT: D 3 GLN cc_start: 0.8185 (mt0) cc_final: 0.7758 (tt0) REVERT: D 105 GLN cc_start: 0.7335 (mp10) cc_final: 0.6664 (pm20) REVERT: E 46 GLU cc_start: 0.7615 (tt0) cc_final: 0.6409 (pm20) REVERT: F 81 GLU cc_start: 0.5889 (mp0) cc_final: 0.5637 (pt0) REVERT: F 103 ARG cc_start: 0.8454 (ttm110) cc_final: 0.7945 (mtt90) REVERT: G 61 ARG cc_start: 0.6671 (ptt-90) cc_final: 0.6335 (ptt-90) REVERT: H 46 GLU cc_start: 0.7545 (tt0) cc_final: 0.5952 (pm20) REVERT: H 91 TYR cc_start: 0.7785 (m-80) cc_final: 0.7261 (m-80) REVERT: H 105 GLN cc_start: 0.7474 (mp10) cc_final: 0.6890 (pm20) REVERT: L 89 GLN cc_start: 0.7510 (tt0) cc_final: 0.6848 (tt0) REVERT: L 103 ARG cc_start: 0.8133 (ttm110) cc_final: 0.7807 (mtt90) outliers start: 49 outliers final: 34 residues processed: 269 average time/residue: 0.1468 time to fit residues: 59.0910 Evaluate side-chains 261 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 226 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 346 MET Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 402 LEU 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 290 THR Chi-restraints excluded: chain B residue 347 VAL 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 290 THR Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 37 ILE 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 108 LEU 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 84 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 454 GLN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 ASN C 355 HIS ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** F 34 ASN ** 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 = 0.4004 r_free = 0.4004 target = 0.166215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.138803 restraints weight = 22215.588| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.02 r_work: 0.3544 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 17544 Z= 0.338 Angle : 0.801 14.913 23814 Z= 0.410 Chirality : 0.050 0.216 2589 Planarity : 0.005 0.047 3057 Dihedral : 6.124 46.624 2649 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.17 % Allowed : 11.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.17), residues: 2118 helix: 1.08 (0.27), residues: 345 sheet: -0.72 (0.21), residues: 564 loop : -0.95 (0.16), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 262A TYR 0.029 0.003 TYR G 49 PHE 0.026 0.003 PHE B 439 TRP 0.023 0.003 TRP B 69 HIS 0.020 0.003 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00815 (17505) covalent geometry : angle 0.79231 (23721) SS BOND : bond 0.00792 ( 24) SS BOND : angle 1.65408 ( 48) hydrogen bonds : bond 0.04313 ( 663) hydrogen bonds : angle 6.15545 ( 1863) link_BETA1-4 : bond 0.00597 ( 3) link_BETA1-4 : angle 1.60877 ( 9) link_NAG-ASN : bond 0.00437 ( 12) link_NAG-ASN : angle 2.56316 ( 36) *********************** 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 298 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 239 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8563 (ttp) cc_final: 0.8316 (ttp) REVERT: A 408 ASN cc_start: 0.9036 (t0) cc_final: 0.8634 (t0) REVERT: B 84 TRP cc_start: 0.8189 (OUTLIER) cc_final: 0.7441 (m-10) REVERT: B 176 MET cc_start: 0.8643 (ttm) cc_final: 0.8317 (ttm) REVERT: B 434 GLU cc_start: 0.8023 (tp30) cc_final: 0.7788 (tp30) REVERT: C 151 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8228 (mmt) REVERT: C 419 ASP cc_start: 0.8517 (m-30) cc_final: 0.8224 (m-30) REVERT: D 3 GLN cc_start: 0.8204 (mt0) cc_final: 0.7873 (tt0) REVERT: D 105 GLN cc_start: 0.7729 (mp10) cc_final: 0.6837 (pm20) REVERT: E 46 GLU cc_start: 0.7581 (tt0) cc_final: 0.6280 (pm20) REVERT: F 61 ARG cc_start: 0.6764 (ptt-90) cc_final: 0.6501 (ptt-90) REVERT: F 103 ARG cc_start: 0.8518 (ttm110) cc_final: 0.8151 (mtt90) REVERT: G 61 ARG cc_start: 0.6809 (ptt-90) cc_final: 0.6510 (ptt-90) REVERT: G 79 GLN cc_start: 0.6916 (mm-40) cc_final: 0.6577 (mm110) REVERT: H 105 GLN cc_start: 0.7657 (mp10) cc_final: 0.6953 (pm20) REVERT: L 103 ARG cc_start: 0.8442 (ttm110) cc_final: 0.8036 (mtt90) outliers start: 59 outliers final: 41 residues processed: 274 average time/residue: 0.1573 time to fit residues: 63.4269 Evaluate side-chains 262 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 219 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR 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 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 113 SER 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 323 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 46 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 197 ASN Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 355 HIS Chi-restraints excluded: chain C residue 447 LEU 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 50 TYR 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 53 THR Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 67 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 130 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 146 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 ASN C 410 ASN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.170705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143171 restraints weight = 21877.144| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.04 r_work: 0.3613 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4244 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= 0.145 Angle : 0.614 11.994 23814 Z= 0.317 Chirality : 0.044 0.200 2589 Planarity : 0.004 0.034 3057 Dihedral : 5.614 43.073 2649 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.36 % Allowed : 12.88 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.17), residues: 2118 helix: 1.36 (0.27), residues: 345 sheet: -0.63 (0.21), residues: 555 loop : -0.91 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 81 TYR 0.026 0.002 TYR B 105 PHE 0.014 0.002 PHE C 439 TRP 0.021 0.001 TRP B 153 HIS 0.025 0.002 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00338 (17505) covalent geometry : angle 0.60538 (23721) SS BOND : bond 0.00368 ( 24) SS BOND : angle 1.34255 ( 48) hydrogen bonds : bond 0.03694 ( 663) hydrogen bonds : angle 5.74890 ( 1863) link_BETA1-4 : bond 0.00354 ( 3) link_BETA1-4 : angle 1.52808 ( 9) link_NAG-ASN : bond 0.00229 ( 12) link_NAG-ASN : angle 2.20415 ( 36) *********************** 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 273 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 229 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8927 (mtmt) cc_final: 0.8536 (mttp) REVERT: A 268 MET cc_start: 0.8066 (ttm) cc_final: 0.7373 (ttm) REVERT: A 412 LYS cc_start: 0.8479 (tmtt) cc_final: 0.8244 (tmtt) REVERT: A 456 ARG cc_start: 0.7700 (mmm-85) cc_final: 0.6384 (mtm110) REVERT: B 176 MET cc_start: 0.8486 (ttm) cc_final: 0.8179 (ttm) REVERT: B 478 MET cc_start: 0.7319 (mmm) cc_final: 0.7042 (mmt) REVERT: C 91 GLU cc_start: 0.8088 (tp30) cc_final: 0.7755 (mt-10) REVERT: C 151 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.8102 (mmt) REVERT: C 419 ASP cc_start: 0.8474 (m-30) cc_final: 0.8098 (m-30) REVERT: D 3 GLN cc_start: 0.8154 (mt0) cc_final: 0.7918 (tt0) REVERT: D 105 GLN cc_start: 0.7663 (mp10) cc_final: 0.6991 (pm20) REVERT: E 46 GLU cc_start: 0.7579 (tt0) cc_final: 0.6322 (pm20) REVERT: F 103 ARG cc_start: 0.8434 (ttm110) cc_final: 0.8088 (mtt90) REVERT: G 61 ARG cc_start: 0.6823 (ptt-90) cc_final: 0.6603 (ptt-90) REVERT: H 105 GLN cc_start: 0.7653 (mp10) cc_final: 0.6969 (pm20) REVERT: L 103 ARG cc_start: 0.8288 (ttm110) cc_final: 0.7926 (mtt90) outliers start: 44 outliers final: 31 residues processed: 259 average time/residue: 0.1519 time to fit residues: 58.6472 Evaluate side-chains 249 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 56 ILE 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 462 LEU 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 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 37 ILE Chi-restraints excluded: chain E residue 50 TYR 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 200 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 68 optimal weight: 0.0670 chunk 202 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 180 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.172643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.145248 restraints weight = 21984.859| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.04 r_work: 0.3609 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17544 Z= 0.126 Angle : 0.589 13.781 23814 Z= 0.303 Chirality : 0.043 0.190 2589 Planarity : 0.004 0.037 3057 Dihedral : 5.296 39.375 2649 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.99 % Allowed : 12.99 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.17), residues: 2118 helix: 1.51 (0.27), residues: 345 sheet: -0.39 (0.22), residues: 525 loop : -0.85 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 81 TYR 0.024 0.001 TYR B 105 PHE 0.014 0.002 PHE F 32 TRP 0.022 0.001 TRP D 47 HIS 0.018 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00295 (17505) covalent geometry : angle 0.58120 (23721) SS BOND : bond 0.00318 ( 24) SS BOND : angle 1.28711 ( 48) hydrogen bonds : bond 0.03572 ( 663) hydrogen bonds : angle 5.56849 ( 1863) link_BETA1-4 : bond 0.00294 ( 3) link_BETA1-4 : angle 1.53091 ( 9) link_NAG-ASN : bond 0.00222 ( 12) link_NAG-ASN : angle 2.09495 ( 36) *********************** 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 283 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 246 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8329 (pt0) cc_final: 0.8114 (pt0) REVERT: A 268 MET cc_start: 0.8069 (ttm) cc_final: 0.7375 (ttm) REVERT: A 368 GLU cc_start: 0.7661 (mp0) cc_final: 0.7310 (mp0) REVERT: A 412 LYS cc_start: 0.8404 (tmtt) cc_final: 0.7470 (mtpp) REVERT: A 456 ARG cc_start: 0.7630 (mmm-85) cc_final: 0.6352 (mtm110) REVERT: B 176 MET cc_start: 0.8431 (ttm) cc_final: 0.8159 (ttm) REVERT: C 151 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.8017 (mmt) REVERT: C 419 ASP cc_start: 0.8489 (m-30) cc_final: 0.8111 (m-30) REVERT: D 3 GLN cc_start: 0.8122 (mt0) cc_final: 0.7920 (tt0) REVERT: E 46 GLU cc_start: 0.7554 (tt0) cc_final: 0.6251 (pm20) REVERT: E 76 ASN cc_start: 0.7109 (m-40) cc_final: 0.6753 (m-40) REVERT: F 103 ARG cc_start: 0.8440 (ttm110) cc_final: 0.7959 (mtt90) REVERT: H 105 GLN cc_start: 0.7647 (mp10) cc_final: 0.6965 (pm20) REVERT: L 103 ARG cc_start: 0.8201 (ttm110) cc_final: 0.7911 (mtt90) outliers start: 37 outliers final: 28 residues processed: 271 average time/residue: 0.1510 time to fit residues: 60.4021 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 : 0.650 ------------------------------------------------------------------------------- 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 290 THR 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 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 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 78 LEU 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 108 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 54 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 192 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 197 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 120 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 83 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 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 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN E 100EASN ** H 35BASN ** 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 = 0.4058 r_free = 0.4058 target = 0.170828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.143828 restraints weight = 21825.320| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.00 r_work: 0.3616 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17544 Z= 0.144 Angle : 0.597 12.471 23814 Z= 0.306 Chirality : 0.043 0.215 2589 Planarity : 0.004 0.040 3057 Dihedral : 5.221 37.818 2649 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.93 % Allowed : 13.26 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.17), residues: 2118 helix: 1.39 (0.27), residues: 351 sheet: -0.51 (0.22), residues: 558 loop : -0.90 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 81 TYR 0.022 0.002 TYR B 105 PHE 0.015 0.002 PHE C 439 TRP 0.017 0.001 TRP D 47 HIS 0.017 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00342 (17505) covalent geometry : angle 0.58899 (23721) SS BOND : bond 0.00359 ( 24) SS BOND : angle 1.31703 ( 48) hydrogen bonds : bond 0.03597 ( 663) hydrogen bonds : angle 5.56857 ( 1863) link_BETA1-4 : bond 0.00372 ( 3) link_BETA1-4 : angle 1.53026 ( 9) link_NAG-ASN : bond 0.00249 ( 12) link_NAG-ASN : angle 2.06951 ( 36) *********************** 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 282 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8329 (pt0) cc_final: 0.8085 (pt0) REVERT: A 268 MET cc_start: 0.8073 (ttm) cc_final: 0.7380 (ttm) REVERT: A 374 PHE cc_start: 0.8613 (t80) cc_final: 0.8378 (t80) REVERT: A 412 LYS cc_start: 0.8444 (tmtt) cc_final: 0.7483 (mtpp) REVERT: A 456 ARG cc_start: 0.7727 (mmm-85) cc_final: 0.6276 (mtm110) REVERT: B 176 MET cc_start: 0.8453 (ttm) cc_final: 0.8145 (ttm) REVERT: B 478 MET cc_start: 0.7276 (mmm) cc_final: 0.6438 (mmt) REVERT: C 419 ASP cc_start: 0.8479 (m-30) cc_final: 0.8189 (m-30) REVERT: D 3 GLN cc_start: 0.8173 (mt0) cc_final: 0.7943 (tt0) REVERT: E 46 GLU cc_start: 0.7521 (tt0) cc_final: 0.6237 (pm20) REVERT: F 103 ARG cc_start: 0.8383 (ttm110) cc_final: 0.7931 (mtt90) REVERT: H 105 GLN cc_start: 0.7650 (mp10) cc_final: 0.6970 (pm20) REVERT: L 103 ARG cc_start: 0.8211 (ttm110) cc_final: 0.7931 (mtt90) outliers start: 36 outliers final: 31 residues processed: 270 average time/residue: 0.1392 time to fit residues: 55.7371 Evaluate side-chains 266 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 235 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 290 THR 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 81 SER 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 323 VAL 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 125 ASP Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain D residue 78 LEU 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 108 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 54 LEU 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 190 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 66 optimal weight: 0.4980 chunk 81 optimal weight: 0.6980 chunk 166 optimal weight: 0.0670 chunk 70 optimal weight: 0.3980 chunk 68 optimal weight: 0.4980 chunk 108 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS C 355 HIS ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35BASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.173357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.146535 restraints weight = 21607.713| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.99 r_work: 0.3650 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17544 Z= 0.111 Angle : 0.565 12.226 23814 Z= 0.290 Chirality : 0.043 0.201 2589 Planarity : 0.004 0.040 3057 Dihedral : 5.022 34.133 2649 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.66 % Allowed : 13.53 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.18), residues: 2118 helix: 1.49 (0.27), residues: 351 sheet: -0.37 (0.22), residues: 558 loop : -0.85 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 81 TYR 0.014 0.001 TYR H 50 PHE 0.013 0.001 PHE C 439 TRP 0.020 0.001 TRP D 47 HIS 0.025 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00255 (17505) covalent geometry : angle 0.55721 (23721) SS BOND : bond 0.00255 ( 24) SS BOND : angle 1.28090 ( 48) hydrogen bonds : bond 0.03456 ( 663) hydrogen bonds : angle 5.44152 ( 1863) link_BETA1-4 : bond 0.00256 ( 3) link_BETA1-4 : angle 1.53430 ( 9) link_NAG-ASN : bond 0.00224 ( 12) link_NAG-ASN : angle 1.94741 ( 36) ********************** 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 277 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 246 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 MET cc_start: 0.8072 (ttm) cc_final: 0.7374 (ttm) REVERT: A 368 GLU cc_start: 0.7651 (mp0) cc_final: 0.7297 (mp0) REVERT: A 374 PHE cc_start: 0.8580 (t80) cc_final: 0.8347 (t80) REVERT: A 412 LYS cc_start: 0.8429 (tmtt) cc_final: 0.7491 (mtpp) REVERT: A 454 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7272 (tt0) REVERT: A 456 ARG cc_start: 0.7637 (mmm-85) cc_final: 0.6119 (mtm110) REVERT: B 321 ARG cc_start: 0.8022 (ttm110) cc_final: 0.7548 (ptp-110) REVERT: B 478 MET cc_start: 0.7103 (mmm) cc_final: 0.6407 (mmt) REVERT: C 419 ASP cc_start: 0.8473 (m-30) cc_final: 0.8183 (m-30) REVERT: D 3 GLN cc_start: 0.8196 (mt0) cc_final: 0.7944 (tt0) REVERT: E 46 GLU cc_start: 0.7512 (tt0) cc_final: 0.6252 (pm20) REVERT: F 103 ARG cc_start: 0.8362 (ttm110) cc_final: 0.7980 (mtt90) REVERT: H 91 TYR cc_start: 0.7750 (m-80) cc_final: 0.7275 (m-80) REVERT: H 105 GLN cc_start: 0.7673 (mp10) cc_final: 0.6997 (pm20) REVERT: L 103 ARG cc_start: 0.8178 (ttm110) cc_final: 0.7968 (mtt90) outliers start: 31 outliers final: 26 residues processed: 266 average time/residue: 0.1358 time to fit residues: 53.9530 Evaluate side-chains 264 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 290 THR Chi-restraints excluded: chain A residue 454 GLN 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 113 SER Chi-restraints excluded: chain B residue 198 VAL 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 78 LEU 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 60 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 54 LEU 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 92 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 144 optimal weight: 0.2980 chunk 132 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35BASN ** 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 = 0.4067 r_free = 0.4067 target = 0.171479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.144486 restraints weight = 21793.691| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.99 r_work: 0.3650 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17544 Z= 0.145 Angle : 0.595 12.538 23814 Z= 0.303 Chirality : 0.043 0.200 2589 Planarity : 0.004 0.038 3057 Dihedral : 5.038 33.359 2649 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.72 % Allowed : 13.63 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.18), residues: 2118 helix: 1.47 (0.27), residues: 351 sheet: -0.41 (0.22), residues: 558 loop : -0.91 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 81 TYR 0.028 0.002 TYR B 105 PHE 0.015 0.002 PHE B 439 TRP 0.017 0.001 TRP D 47 HIS 0.006 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00343 (17505) covalent geometry : angle 0.58782 (23721) SS BOND : bond 0.00358 ( 24) SS BOND : angle 1.25385 ( 48) hydrogen bonds : bond 0.03565 ( 663) hydrogen bonds : angle 5.47319 ( 1863) link_BETA1-4 : bond 0.00263 ( 3) link_BETA1-4 : angle 1.49959 ( 9) link_NAG-ASN : bond 0.00260 ( 12) link_NAG-ASN : angle 1.97395 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4323.12 seconds wall clock time: 75 minutes 5.51 seconds (4505.51 seconds total)