Starting phenix.real_space_refine on Sat Jul 4 00:22:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8tp9_41470/07_2026/8tp9_41470.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tp9_41470/07_2026/8tp9_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_41470/07_2026/8tp9_41470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tp9_41470/07_2026/8tp9_41470.map" model { file = "/net/cci-nas-00/data/ceres_data/8tp9_41470/07_2026/8tp9_41470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tp9_41470/07_2026/8tp9_41470.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8tp9_41470/07_2026/8tp9_41470.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8tp9_41470/07_2026/8tp9_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-dev-6108/lib/python3.11/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 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 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 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 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 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 chiralities: 3 Time building chain proxies: 3.82, per 1000 atoms: 0.22 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: 1.58 Conformation dependent library (CDL) restraints added in 647.4 milliseconds 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: 0.59 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: 3.01 Time building geometry restraints manager: 2.05 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: 9890 17.52 - 35.04: 296 35.04 - 52.56: 64 52.56 - 70.09: 55 70.09 - 87.61: 15 Dihedral angle restraints: 10320 sinusoidal: 4188 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 10317 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.620 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: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.790 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 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 : 10.977 87.607 6348 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 are 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/Z covalent geometry : bond 0.02023 / 1.08 (17505) covalent geometry : angle 1.81796 / 1.20 (23721) SS BOND : bond 0.00875 / 0.54 ( 24) SS BOND : angle 2.95803 / 1.91 ( 48) hydrogen bonds : bond 0.12850 / 8.62 ( 663) hydrogen bonds : angle 7.77842 / 5.49 ( 1863) link_BETA1-4 : bond 0.07189 / 3.60 ( 3) link_BETA1-4 : angle 5.36445 / 2.42 ( 9) link_NAG-ASN : bond 0.07409 / 4.62 ( 12) link_NAG-ASN : angle 2.86706 / 1.71 ( 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 : 0.485 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: 0.1334 time to fit residues: 87.4109 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 : 0.722 ------------------------------------------------------------------------------- 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... 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.176767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.149522 restraints weight = 21765.985| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.11 r_work: 0.3685 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17544 Z= 0.175 Angle : 0.715 11.129 23814 Z= 0.379 Chirality : 0.047 0.216 2589 Planarity : 0.004 0.044 3057 Dihedral : 5.928 66.399 2334 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.50 % Allowed : 7.14 % Favored : 91.36 % 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 are not related in a simple way. whole: 0.46 (0.17), residues: 2118 helix: 1.90 (0.27), residues: 321 sheet: 0.40 (0.21), residues: 558 loop : -0.11 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 61 TYR 0.027 0.002 TYR A 105 PHE 0.021 0.002 PHE G 32 TRP 0.026 0.002 TRP B 84 HIS 0.010 0.002 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (17505) covalent geometry : angle 0.70616 / 0.38 (23721) SS BOND : bond 0.00478 / 0.28 ( 24) SS BOND : angle 1.24246 / 0.83 ( 48) hydrogen bonds : bond 0.04588 / 2.97 ( 663) hydrogen bonds : angle 6.11239 / 4.28 ( 1863) link_BETA1-4 : bond 0.00193 / 0.10 ( 3) link_BETA1-4 : angle 2.24516 / 1.34 ( 9) link_NAG-ASN : bond 0.00545 / 0.31 ( 12) link_NAG-ASN : angle 2.53110 / 1.80 ( 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 331 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 303 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8104 (pt0) cc_final: 0.7575 (pt0) REVERT: A 53 LYS cc_start: 0.8840 (mtmt) cc_final: 0.8517 (mttp) REVERT: A 114 SER cc_start: 0.7852 (m) cc_final: 0.7600 (p) REVERT: A 147 PHE cc_start: 0.8083 (t80) cc_final: 0.7547 (t80) REVERT: A 268 MET cc_start: 0.8127 (ttm) cc_final: 0.7364 (ttm) REVERT: A 456 ARG cc_start: 0.7611 (mtt180) cc_final: 0.6743 (mtm110) REVERT: A 460 LYS cc_start: 0.8245 (pttt) cc_final: 0.7723 (ptmm) REVERT: B 147 PHE cc_start: 0.8010 (t80) cc_final: 0.7749 (t80) REVERT: B 176 MET cc_start: 0.8283 (ttm) cc_final: 0.8059 (ttm) REVERT: B 211 LYS cc_start: 0.8059 (tttm) cc_final: 0.7725 (ttmm) REVERT: B 460 LYS cc_start: 0.8547 (pttt) cc_final: 0.7953 (ptmm) REVERT: C 53 LYS cc_start: 0.9032 (mtmt) cc_final: 0.8762 (mttp) REVERT: C 151 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7534 (mmt) REVERT: C 379 ASN cc_start: 0.8223 (m-40) cc_final: 0.7948 (m110) REVERT: C 460 LYS cc_start: 0.8297 (pttt) cc_final: 0.8079 (ptmt) REVERT: D 11 LEU cc_start: 0.8335 (mp) cc_final: 0.8002 (tp) REVERT: D 105 GLN cc_start: 0.7082 (mp10) cc_final: 0.6530 (pm20) REVERT: G 61 ARG cc_start: 0.6722 (ptt-90) cc_final: 0.6211 (ptt-90) REVERT: H 46 GLU cc_start: 0.6907 (pm20) cc_final: 0.6664 (tt0) REVERT: H 105 GLN cc_start: 0.7449 (mp10) cc_final: 0.6851 (pm20) REVERT: L 61 ARG cc_start: 0.6883 (ptt-90) cc_final: 0.6506 (ptt-90) outliers start: 28 outliers final: 11 residues processed: 318 average time/residue: 0.1210 time to fit residues: 57.7643 Evaluate side-chains 254 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 242 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain C residue 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: 4.9990 chunk 202 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 75 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 ASN 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 38 GLN G 38 GLN H 39 GLN L 38 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.172065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.146203 restraints weight = 21882.556| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.01 r_work: 0.3649 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17544 Z= 0.158 Angle : 0.631 10.779 23814 Z= 0.331 Chirality : 0.044 0.217 2589 Planarity : 0.004 0.033 3057 Dihedral : 5.598 62.552 2334 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.36 % Allowed : 9.23 % Favored : 88.41 % 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 are not related in a simple way. whole: 0.25 (0.17), residues: 2118 helix: 1.77 (0.27), residues: 327 sheet: 0.17 (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 0.024 0.002 TYR B 105 PHE 0.029 0.002 PHE C 147 TRP 0.015 0.002 TRP C 84 HIS 0.009 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (17505) covalent geometry : angle 0.62319 / 0.33 (23721) SS BOND : bond 0.00370 / 0.22 ( 24) SS BOND : angle 1.18767 / 0.79 ( 48) hydrogen bonds : bond 0.04009 / 2.59 ( 663) hydrogen bonds : angle 5.77197 / 4.03 ( 1863) link_BETA1-4 : bond 0.00505 / 0.26 ( 3) link_BETA1-4 : angle 1.65650 / 0.92 ( 9) link_NAG-ASN : bond 0.00320 / 0.19 ( 12) link_NAG-ASN : angle 2.24112 / 1.55 ( 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 325 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 281 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8144 (pt0) cc_final: 0.7557 (pt0) REVERT: A 147 PHE cc_start: 0.8214 (t80) cc_final: 0.7844 (t80) REVERT: A 412 LYS cc_start: 0.8389 (tmtt) cc_final: 0.7634 (mtmt) REVERT: A 456 ARG cc_start: 0.7737 (mtt180) cc_final: 0.6783 (mtm110) REVERT: A 482 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7637 (ttpt) REVERT: B 147 PHE cc_start: 0.8123 (t80) cc_final: 0.7882 (t80) REVERT: B 176 MET cc_start: 0.8399 (ttm) cc_final: 0.8131 (ttm) REVERT: B 211 LYS cc_start: 0.8123 (tttm) cc_final: 0.7834 (ttmm) REVERT: C 53 LYS cc_start: 0.9036 (mtmt) cc_final: 0.8733 (mttp) REVERT: C 151 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7617 (mmt) REVERT: C 276 ASN cc_start: 0.8614 (t0) cc_final: 0.8372 (t0) REVERT: C 379 ASN cc_start: 0.8251 (m-40) cc_final: 0.7943 (m110) REVERT: C 419 ASP cc_start: 0.8459 (m-30) cc_final: 0.8120 (m-30) REVERT: C 478 MET cc_start: 0.6994 (mmt) cc_final: 0.6573 (mmt) REVERT: D 105 GLN cc_start: 0.7338 (mp10) cc_final: 0.6621 (pm20) REVERT: E 46 GLU cc_start: 0.7641 (tt0) cc_final: 0.6468 (pm20) REVERT: F 103 ARG cc_start: 0.8443 (ttm110) cc_final: 0.7800 (mtt90) REVERT: G 61 ARG cc_start: 0.6595 (ptt-90) cc_final: 0.6252 (ptt-90) REVERT: H 46 GLU cc_start: 0.7051 (pm20) cc_final: 0.6813 (tt0) REVERT: H 91 TYR cc_start: 0.7789 (m-80) cc_final: 0.7234 (m-80) REVERT: H 105 GLN cc_start: 0.7494 (mp10) cc_final: 0.6930 (pm20) outliers start: 44 outliers final: 28 residues processed: 302 average time/residue: 0.1284 time to fit residues: 58.6907 Evaluate side-chains 260 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 230 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 46 THR Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain 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 78 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 123 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 205 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 198 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 ASN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 HIS C 454 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.172376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.144656 restraints weight = 22017.827| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.14 r_work: 0.3616 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3458 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= 0.151 Angle : 0.616 11.963 23814 Z= 0.317 Chirality : 0.043 0.212 2589 Planarity : 0.004 0.037 3057 Dihedral : 5.414 58.404 2334 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.47 % Allowed : 10.47 % Favored : 87.06 % 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 are not related in a simple way. whole: -0.04 (0.17), residues: 2118 helix: 1.47 (0.26), residues: 345 sheet: -0.11 (0.21), residues: 570 loop : -0.37 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 103 TYR 0.029 0.002 TYR A 105 PHE 0.017 0.002 PHE A 439 TRP 0.013 0.001 TRP C 84 HIS 0.006 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (17505) covalent geometry : angle 0.60115 / 0.31 (23721) SS BOND : bond 0.00378 / 0.23 ( 24) SS BOND : angle 1.48471 / 0.92 ( 48) hydrogen bonds : bond 0.03784 / 2.44 ( 663) hydrogen bonds : angle 5.66979 / 3.98 ( 1863) link_BETA1-4 : bond 0.00358 / 0.18 ( 3) link_BETA1-4 : angle 1.38480 / 0.82 ( 9) link_NAG-ASN : bond 0.00303 / 0.21 ( 12) link_NAG-ASN : angle 3.10972 / 2.51 ( 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 297 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 251 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8225 (pt0) cc_final: 0.7691 (pt0) REVERT: A 147 PHE cc_start: 0.8209 (t80) cc_final: 0.7710 (t80) REVERT: A 412 LYS cc_start: 0.8392 (tmtt) cc_final: 0.7639 (mtmt) REVERT: A 456 ARG cc_start: 0.7949 (mtt180) cc_final: 0.6786 (mtm110) REVERT: A 482 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7626 (ttpt) REVERT: B 176 MET cc_start: 0.8450 (ttm) cc_final: 0.8185 (ttm) REVERT: B 211 LYS cc_start: 0.8164 (tttm) cc_final: 0.7859 (ttmm) REVERT: C 53 LYS cc_start: 0.8961 (mtmt) cc_final: 0.8605 (mttp) REVERT: C 151 MET cc_start: 0.8211 (mtt) cc_final: 0.7676 (mmt) REVERT: C 379 ASN cc_start: 0.8315 (m-40) cc_final: 0.7990 (m110) REVERT: C 419 ASP cc_start: 0.8495 (m-30) cc_final: 0.8157 (m-30) REVERT: D 3 GLN cc_start: 0.8194 (mt0) cc_final: 0.7738 (tt0) REVERT: D 105 GLN cc_start: 0.7357 (mp10) cc_final: 0.6631 (pm20) REVERT: E 46 GLU cc_start: 0.7637 (tt0) cc_final: 0.6440 (pm20) REVERT: F 103 ARG cc_start: 0.8487 (ttm110) cc_final: 0.7973 (mtt90) REVERT: G 61 ARG cc_start: 0.6652 (ptt-90) cc_final: 0.6169 (ptt-90) REVERT: H 46 GLU cc_start: 0.7109 (pm20) cc_final: 0.6865 (tt0) REVERT: H 105 GLN cc_start: 0.7475 (mp10) cc_final: 0.6887 (pm20) REVERT: L 103 ARG cc_start: 0.8141 (ttm110) cc_final: 0.7785 (mtt90) outliers start: 46 outliers final: 30 residues processed: 281 average time/residue: 0.1283 time to fit residues: 54.7950 Evaluate side-chains 262 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 231 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 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 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 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 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: 0.9990 chunk 90 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 156 optimal weight: 0.2980 chunk 126 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 ASN A 354 HIS B 454 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.172219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.144429 restraints weight = 21830.865| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.14 r_work: 0.3597 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3717 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= 0.136 Angle : 0.585 11.207 23814 Z= 0.302 Chirality : 0.043 0.171 2589 Planarity : 0.004 0.034 3057 Dihedral : 5.200 53.188 2334 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.63 % Allowed : 11.16 % Favored : 86.21 % 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 are not related in a simple way. whole: -0.17 (0.18), residues: 2118 helix: 1.46 (0.27), residues: 351 sheet: -0.16 (0.21), residues: 591 loop : -0.52 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 103 TYR 0.025 0.002 TYR B 105 PHE 0.016 0.002 PHE A 439 TRP 0.013 0.001 TRP B 153 HIS 0.005 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (17505) covalent geometry : angle 0.57483 / 0.30 (23721) SS BOND : bond 0.00326 / 0.21 ( 24) SS BOND : angle 1.50687 / 1.14 ( 48) hydrogen bonds : bond 0.03632 / 2.34 ( 663) hydrogen bonds : angle 5.51849 / 3.86 ( 1863) link_BETA1-4 : bond 0.00340 / 0.17 ( 3) link_BETA1-4 : angle 1.28608 / 0.77 ( 9) link_NAG-ASN : bond 0.00285 / 0.19 ( 12) link_NAG-ASN : angle 2.27911 / 1.67 ( 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 290 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 241 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.8279 (t80) cc_final: 0.7991 (t80) REVERT: A 268 MET cc_start: 0.8175 (ttm) cc_final: 0.7575 (ttm) REVERT: A 412 LYS cc_start: 0.8447 (tmtt) cc_final: 0.7645 (mtmt) REVERT: A 456 ARG cc_start: 0.7921 (mtt180) cc_final: 0.6754 (mtm110) REVERT: A 482 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7566 (ttpt) REVERT: B 176 MET cc_start: 0.8456 (ttm) cc_final: 0.8187 (ttm) REVERT: B 478 MET cc_start: 0.7252 (mmm) cc_final: 0.6871 (mmt) REVERT: C 151 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7989 (mmt) REVERT: C 419 ASP cc_start: 0.8488 (m-30) cc_final: 0.8233 (m-30) REVERT: D 105 GLN cc_start: 0.7366 (mp10) cc_final: 0.6596 (pm20) REVERT: E 46 GLU cc_start: 0.7594 (tt0) cc_final: 0.6348 (pm20) REVERT: F 61 ARG cc_start: 0.6766 (ptt-90) cc_final: 0.6552 (ptt-90) REVERT: F 103 ARG cc_start: 0.8441 (ttm110) cc_final: 0.8002 (mtt90) REVERT: G 61 ARG cc_start: 0.6547 (ptt-90) cc_final: 0.6153 (ptt-90) REVERT: H 91 TYR cc_start: 0.7778 (m-80) cc_final: 0.7238 (m-80) REVERT: H 105 GLN cc_start: 0.7511 (mp10) cc_final: 0.6896 (pm20) REVERT: L 103 ARG cc_start: 0.8147 (ttm110) cc_final: 0.7819 (mtt90) outliers start: 49 outliers final: 31 residues processed: 274 average time/residue: 0.1215 time to fit residues: 50.3243 Evaluate side-chains 254 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 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 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 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: 1.9990 chunk 41 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 ASN 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 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** 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 = 0.4023 r_free = 0.4023 target = 0.167745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.140468 restraints weight = 22107.391| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.99 r_work: 0.3564 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 17544 Z= 0.344 Angle : 0.789 13.986 23814 Z= 0.403 Chirality : 0.051 0.541 2589 Planarity : 0.005 0.042 3057 Dihedral : 5.727 45.414 2334 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.27 % Allowed : 11.81 % Favored : 84.92 % 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 are not related in a simple way. whole: -0.80 (0.17), residues: 2118 helix: 1.11 (0.27), residues: 345 sheet: -0.71 (0.20), residues: 594 loop : -0.89 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 262a TYR 0.028 0.003 TYR G 49 PHE 0.023 0.003 PHE A 439 TRP 0.022 0.003 TRP B 343 HIS 0.009 0.003 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00827 / 0.34 (17505) covalent geometry : angle 0.77992 / 0.40 (23721) SS BOND : bond 0.00761 / 0.46 ( 24) SS BOND : angle 1.58042 / 1.12 ( 48) hydrogen bonds : bond 0.04242 / 2.78 ( 663) hydrogen bonds : angle 6.05928 / 4.21 ( 1863) link_BETA1-4 : bond 0.00553 / 0.29 ( 3) link_BETA1-4 : angle 1.15009 / 0.66 ( 9) link_NAG-ASN : bond 0.00827 / 0.63 ( 12) link_NAG-ASN : angle 2.77051 / 1.84 ( 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: 61 poor density : 237 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.8403 (t80) cc_final: 0.8062 (t80) REVERT: A 408 ASN cc_start: 0.9013 (t0) cc_final: 0.8599 (t0) REVERT: B 84 TRP cc_start: 0.8143 (OUTLIER) cc_final: 0.7379 (m-10) REVERT: B 176 MET cc_start: 0.8613 (ttm) cc_final: 0.8322 (ttm) REVERT: B 434 GLU cc_start: 0.8008 (tp30) cc_final: 0.7766 (tp30) REVERT: C 151 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8165 (mmt) REVERT: C 379 ASN cc_start: 0.8500 (m-40) cc_final: 0.8225 (m-40) REVERT: C 419 ASP cc_start: 0.8527 (m-30) cc_final: 0.8238 (m-30) REVERT: D 3 GLN cc_start: 0.8180 (mt0) cc_final: 0.7879 (tt0) REVERT: D 105 GLN cc_start: 0.7538 (mp10) cc_final: 0.6774 (pm20) REVERT: E 46 GLU cc_start: 0.7607 (tt0) cc_final: 0.6328 (pm20) REVERT: F 61 ARG cc_start: 0.6679 (ptt-90) cc_final: 0.6445 (ptt-90) REVERT: F 103 ARG cc_start: 0.8528 (ttm110) cc_final: 0.8108 (mtt90) REVERT: G 61 ARG cc_start: 0.6552 (ptt-90) cc_final: 0.6177 (ptt-90) REVERT: G 79 GLN cc_start: 0.6879 (mm-40) cc_final: 0.6576 (mm110) REVERT: H 35 ASN cc_start: 0.8484 (m-40) cc_final: 0.8231 (m-40) REVERT: H 105 GLN cc_start: 0.7610 (mp10) cc_final: 0.6930 (pm20) REVERT: L 103 ARG cc_start: 0.8372 (ttm110) cc_final: 0.7959 (mtt90) outliers start: 61 outliers final: 46 residues processed: 275 average time/residue: 0.1297 time to fit residues: 53.0613 Evaluate side-chains 270 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 222 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 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 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 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 290 THR 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 290 THR Chi-restraints excluded: chain C residue 355 HIS Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 50 TYR 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 53 THR Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 130 optimal weight: 0.1980 chunk 64 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 146 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 454 GLN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 ASN C 410 ASN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4066 r_free = 0.4066 target = 0.171921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.144511 restraints weight = 21870.987| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.04 r_work: 0.3629 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17544 Z= 0.131 Angle : 0.593 11.877 23814 Z= 0.306 Chirality : 0.043 0.183 2589 Planarity : 0.004 0.036 3057 Dihedral : 5.216 41.057 2334 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.15 % Allowed : 13.04 % 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 are not related in a simple way. whole: -0.62 (0.17), residues: 2118 helix: 1.38 (0.27), residues: 345 sheet: -0.55 (0.21), residues: 555 loop : -0.85 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 137 TYR 0.016 0.002 TYR E 50 PHE 0.013 0.002 PHE C 439 TRP 0.020 0.001 TRP B 153 HIS 0.004 0.001 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (17505) covalent geometry : angle 0.58454 / 0.30 (23721) SS BOND : bond 0.00295 / 0.19 ( 24) SS BOND : angle 1.29937 / 0.87 ( 48) hydrogen bonds : bond 0.03597 / 2.32 ( 663) hydrogen bonds : angle 5.64441 / 3.94 ( 1863) link_BETA1-4 : bond 0.00352 / 0.18 ( 3) link_BETA1-4 : angle 1.16891 / 0.75 ( 9) link_NAG-ASN : bond 0.00161 / 0.09 ( 12) link_NAG-ASN : angle 2.25573 / 1.52 ( 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 277 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 237 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8579 (pp) REVERT: A 53 LYS cc_start: 0.8915 (mtmt) cc_final: 0.8515 (mttp) REVERT: A 268 MET cc_start: 0.8084 (ttm) cc_final: 0.7405 (ttm) REVERT: A 412 LYS cc_start: 0.8447 (tmtt) cc_final: 0.8230 (tmtt) REVERT: A 456 ARG cc_start: 0.7690 (mmm-85) cc_final: 0.6257 (mtm110) REVERT: B 176 MET cc_start: 0.8443 (ttm) cc_final: 0.8137 (ttm) REVERT: B 478 MET cc_start: 0.7307 (mmm) cc_final: 0.7047 (mmt) REVERT: C 151 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.8063 (mmt) REVERT: C 379 ASN cc_start: 0.8521 (m-40) cc_final: 0.8241 (m110) REVERT: C 419 ASP cc_start: 0.8504 (m-30) cc_final: 0.8149 (m-30) REVERT: D 3 GLN cc_start: 0.8140 (mt0) cc_final: 0.7923 (tt0) REVERT: D 105 GLN cc_start: 0.7503 (mp10) cc_final: 0.6869 (pm20) REVERT: E 46 GLU cc_start: 0.7607 (tt0) cc_final: 0.6343 (pm20) REVERT: F 61 ARG cc_start: 0.6732 (ptt-90) cc_final: 0.6514 (ptt-90) REVERT: F 103 ARG cc_start: 0.8516 (ttm110) cc_final: 0.8105 (mtt90) REVERT: G 61 ARG cc_start: 0.6519 (ptt-90) cc_final: 0.6146 (ptt-90) REVERT: H 105 GLN cc_start: 0.7635 (mp10) cc_final: 0.6975 (pm20) REVERT: L 103 ARG cc_start: 0.8256 (ttm110) cc_final: 0.7942 (mtt90) outliers start: 40 outliers final: 26 residues processed: 265 average time/residue: 0.1240 time to fit residues: 49.4669 Evaluate side-chains 246 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU 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 304 GLU 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 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 78 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain 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: 7.9990 chunk 57 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 202 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 180 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 24 optimal weight: 0.0000 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.172393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.144888 restraints weight = 22029.221| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.05 r_work: 0.3623 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17544 Z= 0.133 Angle : 0.588 12.710 23814 Z= 0.301 Chirality : 0.043 0.183 2589 Planarity : 0.004 0.036 3057 Dihedral : 4.980 38.358 2334 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.93 % Allowed : 13.04 % 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 are not related in a simple way. whole: -0.59 (0.17), residues: 2118 helix: 1.49 (0.27), residues: 345 sheet: -0.52 (0.21), residues: 558 loop : -0.87 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 137 TYR 0.026 0.002 TYR B 105 PHE 0.015 0.002 PHE A 439 TRP 0.016 0.001 TRP D 47 HIS 0.004 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (17505) covalent geometry : angle 0.58076 / 0.30 (23721) SS BOND : bond 0.00325 / 0.20 ( 24) SS BOND : angle 1.29601 / 0.88 ( 48) hydrogen bonds : bond 0.03554 / 2.29 ( 663) hydrogen bonds : angle 5.55337 / 3.87 ( 1863) link_BETA1-4 : bond 0.00402 / 0.20 ( 3) link_BETA1-4 : angle 1.12559 / 0.68 ( 9) link_NAG-ASN : bond 0.00228 / 0.14 ( 12) link_NAG-ASN : angle 2.05298 / 1.39 ( 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 282 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8568 (pp) REVERT: A 167 SER cc_start: 0.8696 (p) cc_final: 0.8486 (t) REVERT: A 268 MET cc_start: 0.8155 (ttm) cc_final: 0.7475 (ttm) REVERT: A 412 LYS cc_start: 0.8401 (tmtt) cc_final: 0.7467 (mtpp) REVERT: A 456 ARG cc_start: 0.7696 (mmm-85) cc_final: 0.6389 (mtm110) REVERT: B 176 MET cc_start: 0.8429 (ttm) cc_final: 0.8137 (ttm) REVERT: B 478 MET cc_start: 0.7262 (mmm) cc_final: 0.6400 (mmt) REVERT: C 379 ASN cc_start: 0.8476 (m-40) cc_final: 0.8177 (m110) REVERT: C 419 ASP cc_start: 0.8503 (m-30) cc_final: 0.8216 (m-30) REVERT: D 105 GLN cc_start: 0.7520 (mp10) cc_final: 0.6885 (pm20) REVERT: E 46 GLU cc_start: 0.7587 (tt0) cc_final: 0.6284 (pm20) REVERT: E 76 ASN cc_start: 0.7017 (m-40) cc_final: 0.6619 (m-40) REVERT: F 103 ARG cc_start: 0.8453 (ttm110) cc_final: 0.7987 (mtt90) REVERT: G 61 ARG cc_start: 0.6490 (ptt-90) cc_final: 0.6144 (ptt-90) REVERT: G 103 ARG cc_start: 0.8135 (ttm110) cc_final: 0.7758 (mtt90) REVERT: H 105 GLN cc_start: 0.7633 (mp10) cc_final: 0.6970 (pm20) REVERT: L 103 ARG cc_start: 0.8194 (ttm110) cc_final: 0.7906 (mtt90) outliers start: 36 outliers final: 27 residues processed: 269 average time/residue: 0.1337 time to fit residues: 54.1727 Evaluate side-chains 266 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 238 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU 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 346 MET 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 125 ASP Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 108 LEU 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: 0.9980 chunk 110 optimal weight: 0.8980 chunk 197 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 120 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 83 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 HIS ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** 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 = 0.4066 r_free = 0.4066 target = 0.171581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.144661 restraints weight = 21807.563| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.00 r_work: 0.3618 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17544 Z= 0.134 Angle : 0.598 19.557 23814 Z= 0.303 Chirality : 0.043 0.213 2589 Planarity : 0.004 0.041 3057 Dihedral : 4.934 36.670 2334 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.93 % Allowed : 12.94 % Favored : 85.13 % 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 are not related in a simple way. whole: -0.53 (0.18), residues: 2118 helix: 1.50 (0.27), residues: 345 sheet: -0.44 (0.22), residues: 555 loop : -0.83 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 435 TYR 0.026 0.002 TYR B 105 PHE 0.014 0.002 PHE C 439 TRP 0.015 0.001 TRP D 47 HIS 0.004 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (17505) covalent geometry : angle 0.59133 / 0.30 (23721) SS BOND : bond 0.00319 / 0.20 ( 24) SS BOND : angle 1.23552 / 0.85 ( 48) hydrogen bonds : bond 0.03569 / 2.30 ( 663) hydrogen bonds : angle 5.52702 / 3.86 ( 1863) link_BETA1-4 : bond 0.00325 / 0.16 ( 3) link_BETA1-4 : angle 1.13539 / 0.70 ( 9) link_NAG-ASN : bond 0.00229 / 0.14 ( 12) link_NAG-ASN : angle 1.97383 / 1.34 ( 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 281 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 245 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8593 (pp) REVERT: A 268 MET cc_start: 0.8157 (ttm) cc_final: 0.7476 (ttm) REVERT: A 374 PHE cc_start: 0.8628 (t80) cc_final: 0.8398 (t80) REVERT: A 412 LYS cc_start: 0.8440 (tmtt) cc_final: 0.7508 (mtpp) REVERT: A 456 ARG cc_start: 0.7657 (mmm-85) cc_final: 0.6204 (mtm110) REVERT: B 176 MET cc_start: 0.8424 (ttm) cc_final: 0.8120 (ttm) REVERT: C 379 ASN cc_start: 0.8493 (m-40) cc_final: 0.8219 (m110) REVERT: C 419 ASP cc_start: 0.8478 (m-30) cc_final: 0.8187 (m-30) REVERT: E 46 GLU cc_start: 0.7578 (tt0) cc_final: 0.6298 (pm20) REVERT: E 76 ASN cc_start: 0.7020 (m-40) cc_final: 0.6767 (m-40) REVERT: F 103 ARG cc_start: 0.8427 (ttm110) cc_final: 0.7991 (mtt90) REVERT: G 61 ARG cc_start: 0.6501 (ptt-90) cc_final: 0.6165 (ptt-90) REVERT: G 103 ARG cc_start: 0.8085 (ttm110) cc_final: 0.7680 (mtt90) REVERT: H 105 GLN cc_start: 0.7642 (mp10) cc_final: 0.6975 (pm20) REVERT: L 103 ARG cc_start: 0.8158 (ttm110) cc_final: 0.7890 (mtt90) outliers start: 36 outliers final: 29 residues processed: 270 average time/residue: 0.1354 time to fit residues: 54.7253 Evaluate side-chains 267 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 237 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU 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 413 MET 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 125 ASP Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 108 LEU 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: 0.0270 chunk 81 optimal weight: 0.7980 chunk 166 optimal weight: 0.2980 chunk 70 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 HIS B 479 ASN C 197 ASN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35BASN ** 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 = 0.4052 r_free = 0.4052 target = 0.170473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.143804 restraints weight = 21816.632| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 1.97 r_work: 0.3619 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17544 Z= 0.157 Angle : 0.612 13.271 23814 Z= 0.312 Chirality : 0.044 0.208 2589 Planarity : 0.004 0.040 3057 Dihedral : 4.977 36.211 2334 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.77 % Allowed : 13.26 % Favored : 84.97 % 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 are not related in a simple way. whole: -0.66 (0.18), residues: 2118 helix: 1.33 (0.27), residues: 351 sheet: -0.50 (0.22), residues: 558 loop : -0.92 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 137 TYR 0.017 0.002 TYR G 49 PHE 0.016 0.002 PHE A 439 TRP 0.014 0.001 TRP D 47 HIS 0.005 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (17505) covalent geometry : angle 0.60516 / 0.31 (23721) SS BOND : bond 0.00374 / 0.23 ( 24) SS BOND : angle 1.28556 / 0.88 ( 48) hydrogen bonds : bond 0.03617 / 2.34 ( 663) hydrogen bonds : angle 5.56992 / 3.88 ( 1863) link_BETA1-4 : bond 0.00355 / 0.18 ( 3) link_BETA1-4 : angle 1.13312 / 0.70 ( 9) link_NAG-ASN : bond 0.00267 / 0.16 ( 12) link_NAG-ASN : angle 1.96353 / 1.35 ( 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: 33 poor density : 244 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8632 (pp) REVERT: A 268 MET cc_start: 0.8216 (ttm) cc_final: 0.7542 (ttm) REVERT: A 374 PHE cc_start: 0.8639 (t80) cc_final: 0.8408 (t80) REVERT: A 412 LYS cc_start: 0.8432 (tmtt) cc_final: 0.7490 (mtpp) REVERT: A 456 ARG cc_start: 0.7684 (mmm-85) cc_final: 0.6150 (mtm110) REVERT: B 176 MET cc_start: 0.8443 (ttm) cc_final: 0.8124 (ttm) REVERT: B 478 MET cc_start: 0.7199 (mmm) cc_final: 0.6553 (mmt) REVERT: C 91 GLU cc_start: 0.8108 (tp30) cc_final: 0.7798 (mt-10) REVERT: C 379 ASN cc_start: 0.8521 (m-40) cc_final: 0.8257 (m110) REVERT: C 419 ASP cc_start: 0.8480 (m-30) cc_final: 0.8189 (m-30) REVERT: E 46 GLU cc_start: 0.7591 (tt0) cc_final: 0.6308 (pm20) REVERT: E 76 ASN cc_start: 0.7055 (m-40) cc_final: 0.6796 (m-40) REVERT: F 103 ARG cc_start: 0.8427 (ttm110) cc_final: 0.7999 (mtt90) REVERT: G 34 ASN cc_start: 0.8435 (m-40) cc_final: 0.8197 (m110) REVERT: G 61 ARG cc_start: 0.6490 (ptt-90) cc_final: 0.6143 (ptt-90) REVERT: G 103 ARG cc_start: 0.8103 (ttm110) cc_final: 0.7795 (mtt90) REVERT: H 105 GLN cc_start: 0.7640 (mp10) cc_final: 0.6979 (pm20) REVERT: L 103 ARG cc_start: 0.8178 (ttm110) cc_final: 0.7900 (mtt90) outliers start: 33 outliers final: 29 residues processed: 265 average time/residue: 0.1281 time to fit residues: 50.8202 Evaluate side-chains 266 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 236 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU 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 304 GLU Chi-restraints excluded: chain A residue 346 MET 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 25 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 108 LEU 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: 3.9990 chunk 143 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.170791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143030 restraints weight = 21945.647| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.03 r_work: 0.3626 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17544 Z= 0.177 Angle : 0.629 13.674 23814 Z= 0.320 Chirality : 0.044 0.207 2589 Planarity : 0.004 0.037 3057 Dihedral : 5.065 36.745 2334 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.04 % Allowed : 13.20 % 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 are not related in a simple way. whole: -0.73 (0.17), residues: 2118 helix: 1.26 (0.27), residues: 351 sheet: -0.55 (0.21), residues: 558 loop : -0.97 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 137 TYR 0.026 0.002 TYR B 105 PHE 0.017 0.002 PHE A 439 TRP 0.014 0.002 TRP D 47 HIS 0.006 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (17505) covalent geometry : angle 0.62161 / 0.32 (23721) SS BOND : bond 0.00412 / 0.25 ( 24) SS BOND : angle 1.40074 / 0.99 ( 48) hydrogen bonds : bond 0.03661 / 2.37 ( 663) hydrogen bonds : angle 5.62466 / 3.92 ( 1863) link_BETA1-4 : bond 0.00459 / 0.23 ( 3) link_BETA1-4 : angle 1.14151 / 0.71 ( 9) link_NAG-ASN : bond 0.00280 / 0.17 ( 12) link_NAG-ASN : angle 1.95764 / 1.35 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4025.16 seconds wall clock time: 69 minutes 55.74 seconds (4195.74 seconds total)