Starting phenix.real_space_refine on Sun May 18 15:13:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tp9_41470/05_2025/8tp9_41470.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tp9_41470/05_2025/8tp9_41470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tp9_41470/05_2025/8tp9_41470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tp9_41470/05_2025/8tp9_41470.map" model { file = "/net/cci-nas-00/data/ceres_data/8tp9_41470/05_2025/8tp9_41470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tp9_41470/05_2025/8tp9_41470.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 10740 2.51 5 N 2934 2.21 5 O 3357 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17118 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3816 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 19, 'TRANS': 461} Chain breaks: 1 Chain: "B" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3816 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 19, 'TRANS': 461} Chain breaks: 1 Chain: "C" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3816 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 19, 'TRANS': 461} Chain breaks: 1 Chain: "D" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "E" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "F" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "L" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 10.34, per 1000 atoms: 0.60 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: 4.34 Conformation dependent library (CDL) restraints added in 2.1 seconds 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3900 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 51 sheets defined 18.3% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.47 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 125 through 127 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 366 through 386 Processing helix chain 'A' and resid 403 through 456 Processing helix chain 'A' and resid 474 through 482 Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 125 through 127 Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 366 through 386 Processing helix chain 'B' and resid 403 through 456 Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 125 through 127 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 366 through 386 Processing helix chain 'C' and resid 403 through 456 Processing helix chain 'C' and resid 474 through 482 Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.328A pdb=" N LEU A 51 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 59 through 62 removed outlier: 6.176A pdb=" N LEU A 59 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.694A pdb=" N SER A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N TRP A 234 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N HIS A 117 " --> pdb=" O SER A 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.694A pdb=" N SER A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N TRP A 234 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.494A pdb=" N ALA A 138 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N ASN A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 168 Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AB3, first strand: chain 'B' and resid 364 through 365 Processing sheet with id=AB4, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AB5, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.328A pdb=" N LEU B 51 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N CYS B 277 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 59 through 62 removed outlier: 6.176A pdb=" N LEU B 59 " --> pdb=" O MET B 88 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.694A pdb=" N SER B 101 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N TRP B 234 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N HIS B 117 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.694A pdb=" N SER B 101 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N TRP B 234 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 136 through 141 removed outlier: 7.493A pdb=" N ALA B 138 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N ASN B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 164 through 168 Processing sheet with id=AC4, first strand: chain 'B' and resid 286 through 287 Processing sheet with id=AC5, first strand: chain 'C' and resid 364 through 365 Processing sheet with id=AC6, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AC7, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC8, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC9, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.328A pdb=" N LEU C 51 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 59 through 62 removed outlier: 6.176A pdb=" N LEU C 59 " --> pdb=" O MET C 88 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.694A pdb=" N SER C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N TRP C 234 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N HIS C 117 " --> pdb=" O SER C 261 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.694A pdb=" N SER C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N TRP C 234 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.493A pdb=" N ALA C 138 " --> pdb=" O ASN C 144 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N ASN C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 164 through 168 Processing sheet with id=AD6, first strand: chain 'C' and resid 286 through 287 Processing sheet with id=AD7, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.585A pdb=" N TYR D 35 " --> pdb=" O GLU D 95 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 11 through 12 removed outlier: 7.079A pdb=" N CYS D 92 " --> pdb=" O TRP D 103 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TRP D 103 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.585A pdb=" N TYR E 35 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.080A pdb=" N CYS E 92 " --> pdb=" O TRP E 103 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TRP E 103 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AE5, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.529A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA F 84 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.529A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA F 84 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.529A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA G 84 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.529A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA G 84 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.585A pdb=" N TYR H 35 " --> pdb=" O GLU H 95 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.079A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.529A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.529A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 717 hydrogen bonds defined for protein. 1863 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.36 Time building geometry restraints manager: 5.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4168 1.32 - 1.46: 5445 1.46 - 1.60: 7741 1.60 - 1.73: 31 1.73 - 1.87: 120 Bond restraints: 17505 Sorted by residual: bond pdb=" CB HIS B 354 " pdb=" CG HIS B 354 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.11e+01 bond pdb=" CB HIS C 354 " pdb=" CG HIS C 354 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.09e+01 bond pdb=" CB HIS A 354 " pdb=" CG HIS A 354 " ideal model delta sigma weight residual 1.497 1.408 0.089 1.40e-02 5.10e+03 4.07e+01 bond pdb=" CG MET B 151 " pdb=" SD MET B 151 " ideal model delta sigma weight residual 1.803 1.684 0.119 2.50e-02 1.60e+03 2.26e+01 bond pdb=" CG MET C 151 " pdb=" SD MET C 151 " ideal model delta sigma weight residual 1.803 1.684 0.119 2.50e-02 1.60e+03 2.25e+01 ... (remaining 17500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.22: 23660 7.22 - 14.44: 58 14.44 - 21.66: 0 21.66 - 28.89: 0 28.89 - 36.11: 3 Bond angle restraints: 23721 Sorted by residual: angle pdb=" C2 NAG J 1 " pdb=" N2 NAG J 1 " pdb=" C7 NAG J 1 " ideal model delta sigma weight residual 124.56 160.67 -36.11 3.00e+00 1.11e-01 1.45e+02 angle pdb=" C2 NAG K 1 " pdb=" N2 NAG K 1 " pdb=" C7 NAG K 1 " ideal model delta sigma weight residual 124.56 160.66 -36.10 3.00e+00 1.11e-01 1.45e+02 angle pdb=" C2 NAG I 1 " pdb=" N2 NAG I 1 " pdb=" C7 NAG I 1 " ideal model delta sigma weight residual 124.56 160.64 -36.08 3.00e+00 1.11e-01 1.45e+02 angle pdb=" N THR C 318 " pdb=" CA THR C 318 " pdb=" C THR C 318 " ideal model delta sigma weight residual 114.56 103.34 11.22 1.27e+00 6.20e-01 7.80e+01 angle pdb=" N THR B 318 " pdb=" CA THR B 318 " pdb=" C THR B 318 " ideal model delta sigma weight residual 114.56 103.37 11.19 1.27e+00 6.20e-01 7.76e+01 ... (remaining 23716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 10196 17.52 - 35.04: 299 35.04 - 52.56: 64 52.56 - 70.09: 61 70.09 - 87.61: 15 Dihedral angle restraints: 10635 sinusoidal: 4503 harmonic: 6132 Sorted by residual: dihedral pdb=" C TRP C 84 " pdb=" N TRP C 84 " pdb=" CA TRP C 84 " pdb=" CB TRP C 84 " ideal model delta harmonic sigma weight residual -122.60 -108.36 -14.24 0 2.50e+00 1.60e-01 3.24e+01 dihedral pdb=" C TRP B 84 " pdb=" N TRP B 84 " pdb=" CA TRP B 84 " pdb=" CB TRP B 84 " ideal model delta harmonic sigma weight residual -122.60 -108.36 -14.24 0 2.50e+00 1.60e-01 3.24e+01 dihedral pdb=" C TRP A 84 " pdb=" N TRP A 84 " pdb=" CA TRP A 84 " pdb=" CB TRP A 84 " ideal model delta harmonic sigma weight residual -122.60 -108.39 -14.21 0 2.50e+00 1.60e-01 3.23e+01 ... (remaining 10632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1764 0.092 - 0.183: 596 0.183 - 0.275: 156 0.275 - 0.367: 49 0.367 - 0.458: 24 Chirality restraints: 2589 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.26e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.25e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.24e+02 ... (remaining 2586 not shown) Planarity restraints: 3069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 84 " 0.102 2.00e-02 2.50e+03 4.84e-02 5.86e+01 pdb=" CG TRP B 84 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 84 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 84 " -0.049 2.00e-02 2.50e+03 pdb=" NE1 TRP B 84 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP B 84 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 84 " -0.054 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 84 " 0.054 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 84 " -0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP B 84 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 84 " -0.102 2.00e-02 2.50e+03 4.84e-02 5.85e+01 pdb=" CG TRP A 84 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A 84 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 84 " 0.049 2.00e-02 2.50e+03 pdb=" NE1 TRP A 84 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP A 84 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 84 " 0.053 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 84 " -0.054 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 84 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP A 84 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 84 " 0.102 2.00e-02 2.50e+03 4.84e-02 5.85e+01 pdb=" CG TRP C 84 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP C 84 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP C 84 " -0.049 2.00e-02 2.50e+03 pdb=" NE1 TRP C 84 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP C 84 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP C 84 " -0.054 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 84 " 0.054 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 84 " -0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP C 84 " 0.044 2.00e-02 2.50e+03 ... (remaining 3066 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 5343 2.85 - 3.36: 15237 3.36 - 3.87: 29165 3.87 - 4.39: 35114 4.39 - 4.90: 57536 Nonbonded interactions: 142395 Sorted by model distance: nonbonded pdb=" O ALA B 336 " pdb=" NE1 TRP B 343 " model vdw 2.334 3.120 nonbonded pdb=" O ALA C 336 " pdb=" NE1 TRP C 343 " model vdw 2.384 3.120 nonbonded pdb=" N THR C 318 " pdb=" N GLY C 319 " model vdw 2.414 2.560 nonbonded pdb=" N THR B 318 " pdb=" N GLY B 319 " model vdw 2.414 2.560 nonbonded pdb=" N THR A 318 " pdb=" N GLY A 319 " model vdw 2.415 2.560 ... (remaining 142390 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 40.920 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.090 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.155 17544 Z= 1.089 Angle : 1.826 36.106 23814 Z= 1.203 Chirality : 0.108 0.458 2589 Planarity : 0.008 0.048 3057 Dihedral : 10.910 87.607 6663 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.17), residues: 2118 helix: 0.41 (0.24), residues: 327 sheet: 0.99 (0.22), residues: 456 loop : 0.33 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.102 0.010 TRP B 84 HIS 0.019 0.003 HIS C 18 PHE 0.036 0.006 PHE C 118 TYR 0.062 0.008 TYR D 50 ARG 0.007 0.001 ARG C 262A Details of bonding type rmsd link_NAG-ASN : bond 0.07409 ( 12) link_NAG-ASN : angle 2.86706 ( 36) link_BETA1-4 : bond 0.07189 ( 3) link_BETA1-4 : angle 5.36445 ( 9) hydrogen bonds : bond 0.12850 ( 663) hydrogen bonds : angle 7.77842 ( 1863) SS BOND : bond 0.00875 ( 24) SS BOND : angle 2.95803 ( 48) covalent geometry : bond 0.02023 (17505) covalent geometry : angle 1.81796 (23721) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 1.791 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: 0.2997 time to fit residues: 194.0764 Evaluate side-chains 250 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS A 196 GLN A 197 ASN A 410 ASN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS B 197 ASN B 424 ASN B 471 HIS C 197 ASN C 424 ASN C 471 HIS F 27 HIS F 34 ASN F 89 GLN G 27 HIS L 27 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.175806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.148491 restraints weight = 21763.524| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.11 r_work: 0.3672 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17544 Z= 0.184 Angle : 0.715 11.334 23814 Z= 0.379 Chirality : 0.047 0.228 2589 Planarity : 0.004 0.036 3057 Dihedral : 6.254 66.356 2649 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.66 % Allowed : 7.19 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.17), residues: 2118 helix: 1.85 (0.27), residues: 321 sheet: 0.35 (0.21), residues: 558 loop : -0.14 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 84 HIS 0.009 0.001 HIS A 355 PHE 0.021 0.003 PHE C 439 TYR 0.027 0.002 TYR A 105 ARG 0.005 0.000 ARG F 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 12) link_NAG-ASN : angle 2.50329 ( 36) link_BETA1-4 : bond 0.00268 ( 3) link_BETA1-4 : angle 2.64283 ( 9) hydrogen bonds : bond 0.04510 ( 663) hydrogen bonds : angle 6.10766 ( 1863) SS BOND : bond 0.00927 ( 24) SS BOND : angle 1.34747 ( 48) covalent geometry : bond 0.00420 (17505) covalent geometry : angle 0.70571 (23721) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 301 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8122 (pt0) cc_final: 0.7587 (pt0) REVERT: A 53 LYS cc_start: 0.8853 (mtmt) cc_final: 0.8519 (mttp) REVERT: A 147 PHE cc_start: 0.8105 (t80) cc_final: 0.7883 (t80) REVERT: A 268 MET cc_start: 0.8129 (ttm) cc_final: 0.7348 (ttm) REVERT: A 412 LYS cc_start: 0.8447 (tmtt) cc_final: 0.7714 (mtmt) REVERT: A 456 ARG cc_start: 0.7622 (mtt180) cc_final: 0.6742 (mtm110) REVERT: A 460 LYS cc_start: 0.8252 (pttt) cc_final: 0.7731 (ptmm) REVERT: B 147 PHE cc_start: 0.8032 (t80) cc_final: 0.7744 (t80) REVERT: B 176 MET cc_start: 0.8323 (ttm) cc_final: 0.8105 (ttm) REVERT: B 211 LYS cc_start: 0.8066 (tttm) cc_final: 0.7733 (ttmm) REVERT: C 53 LYS cc_start: 0.9050 (mtmt) cc_final: 0.8771 (mttp) REVERT: C 151 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7510 (mmt) REVERT: C 276 ASN cc_start: 0.8708 (t0) cc_final: 0.8341 (t0) REVERT: C 379 ASN cc_start: 0.8241 (m-40) cc_final: 0.7962 (m110) REVERT: C 460 LYS cc_start: 0.8300 (pttt) cc_final: 0.8081 (ptmt) REVERT: D 11 LEU cc_start: 0.8312 (mp) cc_final: 0.8032 (tp) REVERT: D 105 GLN cc_start: 0.7101 (mp10) cc_final: 0.6581 (pm20) REVERT: H 105 GLN cc_start: 0.7468 (mp10) cc_final: 0.6860 (pm20) REVERT: L 61 ARG cc_start: 0.6920 (ptt-90) cc_final: 0.6605 (ptt-90) outliers start: 31 outliers final: 12 residues processed: 316 average time/residue: 0.2927 time to fit residues: 137.7069 Evaluate side-chains 261 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 248 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 121 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 192 optimal weight: 0.0470 chunk 142 optimal weight: 0.8980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN B 410 ASN C 244 ASN ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 ASN D 39 GLN E 39 GLN F 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 = 0.4076 r_free = 0.4076 target = 0.174566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.147797 restraints weight = 21754.278| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.07 r_work: 0.3665 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17544 Z= 0.139 Angle : 0.613 11.369 23814 Z= 0.321 Chirality : 0.044 0.210 2589 Planarity : 0.004 0.033 3057 Dihedral : 5.784 62.700 2649 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.15 % Allowed : 9.34 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.17), residues: 2118 helix: 1.80 (0.27), residues: 327 sheet: 0.15 (0.21), residues: 564 loop : -0.14 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 84 HIS 0.008 0.001 HIS A 355 PHE 0.031 0.002 PHE C 147 TYR 0.018 0.002 TYR A 105 ARG 0.004 0.000 ARG F 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 12) link_NAG-ASN : angle 2.23583 ( 36) link_BETA1-4 : bond 0.00528 ( 3) link_BETA1-4 : angle 2.28556 ( 9) hydrogen bonds : bond 0.03965 ( 663) hydrogen bonds : angle 5.73973 ( 1863) SS BOND : bond 0.00790 ( 24) SS BOND : angle 1.11277 ( 48) covalent geometry : bond 0.00317 (17505) covalent geometry : angle 0.60440 (23721) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 275 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8176 (pt0) cc_final: 0.7578 (pt0) REVERT: A 147 PHE cc_start: 0.8176 (t80) cc_final: 0.7708 (t80) REVERT: A 412 LYS cc_start: 0.8409 (tmtt) cc_final: 0.7622 (mtmt) REVERT: A 456 ARG cc_start: 0.7706 (mtt180) cc_final: 0.6756 (mtm110) REVERT: B 147 PHE cc_start: 0.8116 (t80) cc_final: 0.7877 (t80) REVERT: B 176 MET cc_start: 0.8342 (ttm) cc_final: 0.8075 (ttm) REVERT: B 211 LYS cc_start: 0.8130 (tttm) cc_final: 0.7824 (ttmm) REVERT: C 53 LYS cc_start: 0.9029 (mtmt) cc_final: 0.8749 (mttp) REVERT: C 114 SER cc_start: 0.7855 (m) cc_final: 0.7547 (p) REVERT: C 151 MET cc_start: 0.8059 (mtt) cc_final: 0.7524 (mmt) REVERT: C 419 ASP cc_start: 0.8454 (m-30) cc_final: 0.8109 (m-30) REVERT: C 478 MET cc_start: 0.7002 (mmt) cc_final: 0.6561 (mmt) REVERT: D 3 GLN cc_start: 0.8128 (mt0) cc_final: 0.7812 (tt0) REVERT: D 105 GLN cc_start: 0.7159 (mp10) cc_final: 0.6585 (pm20) REVERT: E 46 GLU cc_start: 0.7401 (tt0) cc_final: 0.6433 (pm20) REVERT: G 61 ARG cc_start: 0.6708 (ptp90) cc_final: 0.6219 (ptt-90) REVERT: H 91 TYR cc_start: 0.7839 (m-80) cc_final: 0.7202 (m-80) REVERT: H 105 GLN cc_start: 0.7495 (mp10) cc_final: 0.6946 (pm20) outliers start: 40 outliers final: 25 residues processed: 296 average time/residue: 0.2900 time to fit residues: 128.4933 Evaluate side-chains 257 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 232 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 157 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 164 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 146 optimal weight: 0.0010 chunk 170 optimal weight: 0.9980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 454 GLN B 454 GLN C 110 HIS C 454 GLN ** H 35BASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.173652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.146098 restraints weight = 21794.709| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.14 r_work: 0.3633 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3501 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= 0.131 Angle : 0.588 11.177 23814 Z= 0.303 Chirality : 0.044 0.360 2589 Planarity : 0.004 0.038 3057 Dihedral : 5.569 57.699 2649 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.42 % Allowed : 10.31 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.17), residues: 2118 helix: 1.51 (0.26), residues: 345 sheet: -0.02 (0.21), residues: 564 loop : -0.30 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 84 HIS 0.005 0.001 HIS A 355 PHE 0.018 0.002 PHE C 147 TYR 0.025 0.002 TYR B 105 ARG 0.004 0.000 ARG F 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00657 ( 12) link_NAG-ASN : angle 2.88964 ( 36) link_BETA1-4 : bond 0.00416 ( 3) link_BETA1-4 : angle 2.01843 ( 9) hydrogen bonds : bond 0.03674 ( 663) hydrogen bonds : angle 5.52508 ( 1863) SS BOND : bond 0.00328 ( 24) SS BOND : angle 0.98229 ( 48) covalent geometry : bond 0.00303 (17505) covalent geometry : angle 0.57538 (23721) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 262 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8224 (pt0) cc_final: 0.7707 (pt0) REVERT: A 147 PHE cc_start: 0.8167 (t80) cc_final: 0.7904 (t80) REVERT: A 304 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7355 (pt0) REVERT: A 412 LYS cc_start: 0.8476 (tmtt) cc_final: 0.7688 (mtmt) REVERT: A 456 ARG cc_start: 0.7938 (mtt180) cc_final: 0.6788 (mtm110) REVERT: B 176 MET cc_start: 0.8384 (ttm) cc_final: 0.8113 (ttm) REVERT: B 211 LYS cc_start: 0.8168 (tttm) cc_final: 0.7864 (ttmm) REVERT: C 53 LYS cc_start: 0.9065 (mtmt) cc_final: 0.8762 (mttp) REVERT: C 151 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7925 (mmt) REVERT: C 419 ASP cc_start: 0.8485 (m-30) cc_final: 0.8143 (m-30) REVERT: D 3 GLN cc_start: 0.8191 (mt0) cc_final: 0.7889 (tt0) REVERT: D 105 GLN cc_start: 0.7364 (mp10) cc_final: 0.6649 (pm20) REVERT: E 46 GLU cc_start: 0.7627 (tt0) cc_final: 0.6473 (pm20) REVERT: G 61 ARG cc_start: 0.6687 (ptp90) cc_final: 0.6142 (ptt-90) REVERT: G 89 GLN cc_start: 0.7318 (tm-30) cc_final: 0.6804 (tm-30) REVERT: H 91 TYR cc_start: 0.7822 (m-80) cc_final: 0.7274 (m-80) REVERT: H 105 GLN cc_start: 0.7480 (mp10) cc_final: 0.6930 (pm20) REVERT: H 108 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8243 (tp) outliers start: 45 outliers final: 26 residues processed: 291 average time/residue: 0.2833 time to fit residues: 123.8431 Evaluate side-chains 257 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 228 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 145 optimal weight: 0.0010 chunk 95 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 200 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 156 optimal weight: 0.0870 chunk 15 optimal weight: 4.9990 overall best weight: 1.2168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 354 HIS ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 ASN ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35BASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.169249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.140988 restraints weight = 21994.424| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.15 r_work: 0.3578 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17544 Z= 0.189 Angle : 0.643 12.664 23814 Z= 0.332 Chirality : 0.045 0.182 2589 Planarity : 0.004 0.031 3057 Dihedral : 5.530 50.590 2649 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.79 % Allowed : 11.59 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.17), residues: 2118 helix: 1.47 (0.26), residues: 345 sheet: -0.32 (0.20), residues: 591 loop : -0.63 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 153 HIS 0.007 0.002 HIS A 184 PHE 0.018 0.002 PHE A 439 TYR 0.023 0.002 TYR C 105 ARG 0.005 0.000 ARG F 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 12) link_NAG-ASN : angle 2.33227 ( 36) link_BETA1-4 : bond 0.00619 ( 3) link_BETA1-4 : angle 1.80222 ( 9) hydrogen bonds : bond 0.03790 ( 663) hydrogen bonds : angle 5.68341 ( 1863) SS BOND : bond 0.00474 ( 24) SS BOND : angle 1.57603 ( 48) covalent geometry : bond 0.00448 (17505) covalent geometry : angle 0.63260 (23721) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 251 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.8270 (t80) cc_final: 0.7945 (t80) REVERT: A 268 MET cc_start: 0.8191 (ttm) cc_final: 0.7579 (ttm) REVERT: A 412 LYS cc_start: 0.8503 (tmtt) cc_final: 0.7720 (mtmt) REVERT: A 456 ARG cc_start: 0.7934 (mtt180) cc_final: 0.6951 (mtm110) REVERT: B 176 MET cc_start: 0.8519 (ttm) cc_final: 0.8228 (ttm) REVERT: B 478 MET cc_start: 0.7427 (mmm) cc_final: 0.7005 (mmt) REVERT: C 151 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.8065 (mmt) REVERT: C 419 ASP cc_start: 0.8502 (m-30) cc_final: 0.8242 (m-30) REVERT: D 3 GLN cc_start: 0.8278 (mt0) cc_final: 0.8021 (tt0) REVERT: D 105 GLN cc_start: 0.7433 (mp10) cc_final: 0.6734 (pm20) REVERT: E 46 GLU cc_start: 0.7599 (tt0) cc_final: 0.6389 (pm20) REVERT: G 61 ARG cc_start: 0.6587 (ptp90) cc_final: 0.5933 (ptt180) REVERT: G 82 ASP cc_start: 0.7698 (m-30) cc_final: 0.7094 (m-30) REVERT: G 89 GLN cc_start: 0.7565 (tm-30) cc_final: 0.7355 (tm-30) REVERT: H 105 GLN cc_start: 0.7544 (mp10) cc_final: 0.6946 (pm20) REVERT: L 103 ARG cc_start: 0.8169 (ttm110) cc_final: 0.7801 (mtt90) outliers start: 52 outliers final: 36 residues processed: 283 average time/residue: 0.2890 time to fit residues: 123.0022 Evaluate side-chains 261 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 224 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 25 SER 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 25 SER Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 114 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 97 optimal weight: 0.0470 chunk 203 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.170516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.142664 restraints weight = 21848.580| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.10 r_work: 0.3604 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17544 Z= 0.136 Angle : 0.615 14.347 23814 Z= 0.311 Chirality : 0.043 0.211 2589 Planarity : 0.004 0.031 3057 Dihedral : 5.547 45.016 2649 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.52 % Allowed : 12.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.17), residues: 2118 helix: 1.63 (0.27), residues: 345 sheet: -0.29 (0.21), residues: 558 loop : -0.64 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 47 HIS 0.007 0.001 HIS C 18 PHE 0.015 0.002 PHE C 439 TYR 0.025 0.002 TYR B 105 ARG 0.005 0.000 ARG B 137 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 12) link_NAG-ASN : angle 2.86153 ( 36) link_BETA1-4 : bond 0.00342 ( 3) link_BETA1-4 : angle 1.71675 ( 9) hydrogen bonds : bond 0.03634 ( 663) hydrogen bonds : angle 5.55748 ( 1863) SS BOND : bond 0.00327 ( 24) SS BOND : angle 1.48660 ( 48) covalent geometry : bond 0.00319 (17505) covalent geometry : angle 0.60111 (23721) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 230 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.8318 (t80) cc_final: 0.8036 (t80) REVERT: A 268 MET cc_start: 0.8140 (ttm) cc_final: 0.7495 (ttm) REVERT: A 412 LYS cc_start: 0.8414 (tmtt) cc_final: 0.7457 (mtpp) REVERT: A 456 ARG cc_start: 0.7957 (mtt180) cc_final: 0.6961 (mtm110) REVERT: B 84 TRP cc_start: 0.7899 (OUTLIER) cc_final: 0.7197 (m-10) REVERT: B 176 MET cc_start: 0.8481 (ttm) cc_final: 0.8066 (ttm) REVERT: C 151 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.8050 (mmt) REVERT: C 419 ASP cc_start: 0.8447 (m-30) cc_final: 0.8148 (m-30) REVERT: D 3 GLN cc_start: 0.8229 (mt0) cc_final: 0.7970 (tt0) REVERT: D 105 GLN cc_start: 0.7419 (mp10) cc_final: 0.6706 (pm20) REVERT: E 46 GLU cc_start: 0.7591 (tt0) cc_final: 0.6347 (pm20) REVERT: F 103 ARG cc_start: 0.8455 (ttm110) cc_final: 0.7925 (mtt90) REVERT: G 61 ARG cc_start: 0.6550 (ptp90) cc_final: 0.5999 (ptt-90) REVERT: G 82 ASP cc_start: 0.7697 (m-30) cc_final: 0.7150 (m-30) REVERT: G 89 GLN cc_start: 0.7246 (tm-30) cc_final: 0.6840 (tm-30) REVERT: H 105 GLN cc_start: 0.7594 (mp10) cc_final: 0.6979 (pm20) REVERT: L 103 ARG cc_start: 0.8135 (ttm110) cc_final: 0.7825 (mtt90) outliers start: 47 outliers final: 35 residues processed: 261 average time/residue: 0.2860 time to fit residues: 112.7162 Evaluate side-chains 256 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 219 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 290 THR 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 25 SER Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 181 optimal weight: 0.6980 chunk 131 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 184 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.4010 r_free = 0.4010 target = 0.168676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.141335 restraints weight = 21724.559| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.05 r_work: 0.3590 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4152 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= 0.144 Angle : 0.609 13.736 23814 Z= 0.309 Chirality : 0.044 0.322 2589 Planarity : 0.004 0.034 3057 Dihedral : 5.228 38.537 2649 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.15 % Allowed : 12.56 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.17), residues: 2118 helix: 1.66 (0.27), residues: 345 sheet: -0.29 (0.22), residues: 555 loop : -0.70 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 47 HIS 0.007 0.001 HIS C 18 PHE 0.015 0.002 PHE C 439 TYR 0.026 0.002 TYR A 105 ARG 0.004 0.000 ARG C 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 12) link_NAG-ASN : angle 3.06400 ( 36) link_BETA1-4 : bond 0.00368 ( 3) link_BETA1-4 : angle 1.66501 ( 9) hydrogen bonds : bond 0.03567 ( 663) hydrogen bonds : angle 5.49190 ( 1863) SS BOND : bond 0.00356 ( 24) SS BOND : angle 1.34002 ( 48) covalent geometry : bond 0.00341 (17505) covalent geometry : angle 0.59448 (23721) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 233 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 MET cc_start: 0.8121 (ttm) cc_final: 0.7444 (ttm) REVERT: A 374 PHE cc_start: 0.8599 (t80) cc_final: 0.8360 (t80) REVERT: A 412 LYS cc_start: 0.8370 (tmtt) cc_final: 0.7428 (mtpp) REVERT: A 456 ARG cc_start: 0.7712 (mtt180) cc_final: 0.6825 (mtm110) REVERT: B 84 TRP cc_start: 0.7945 (OUTLIER) cc_final: 0.7138 (m-10) REVERT: B 176 MET cc_start: 0.8488 (ttm) cc_final: 0.8110 (ttm) REVERT: B 478 MET cc_start: 0.7217 (mmm) cc_final: 0.6933 (mmt) REVERT: C 151 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8176 (mmt) REVERT: C 419 ASP cc_start: 0.8442 (m-30) cc_final: 0.8138 (m-30) REVERT: D 105 GLN cc_start: 0.7417 (mp10) cc_final: 0.6781 (pm20) REVERT: E 46 GLU cc_start: 0.7545 (tt0) cc_final: 0.6283 (pm20) REVERT: F 103 ARG cc_start: 0.8470 (ttm110) cc_final: 0.8019 (mtt90) REVERT: G 61 ARG cc_start: 0.6522 (ptp90) cc_final: 0.5967 (ptt-90) REVERT: G 82 ASP cc_start: 0.7800 (m-30) cc_final: 0.7210 (m-30) REVERT: G 89 GLN cc_start: 0.7240 (tm-30) cc_final: 0.6969 (tm-30) REVERT: G 103 ARG cc_start: 0.8116 (ttm110) cc_final: 0.7656 (mtt90) REVERT: H 105 GLN cc_start: 0.7609 (mp10) cc_final: 0.6966 (pm20) REVERT: L 103 ARG cc_start: 0.8199 (ttm110) cc_final: 0.7920 (mtt90) outliers start: 40 outliers final: 33 residues processed: 260 average time/residue: 0.3134 time to fit residues: 121.6034 Evaluate side-chains 256 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 221 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain 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 25 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 14 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 188 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 147 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS A 454 GLN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** 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 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.167631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.140542 restraints weight = 21868.072| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.99 r_work: 0.3574 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 17544 Z= 0.245 Angle : 0.702 13.942 23814 Z= 0.358 Chirality : 0.047 0.196 2589 Planarity : 0.005 0.036 3057 Dihedral : 5.535 38.729 2649 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.68 % Allowed : 12.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.17), residues: 2118 helix: 1.43 (0.27), residues: 345 sheet: -0.60 (0.21), residues: 555 loop : -0.92 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 47 HIS 0.009 0.002 HIS C 18 PHE 0.018 0.002 PHE B 439 TYR 0.023 0.002 TYR D 50 ARG 0.004 0.001 ARG C 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00362 ( 12) link_NAG-ASN : angle 2.40576 ( 36) link_BETA1-4 : bond 0.00376 ( 3) link_BETA1-4 : angle 1.49656 ( 9) hydrogen bonds : bond 0.03929 ( 663) hydrogen bonds : angle 5.80145 ( 1863) SS BOND : bond 0.00584 ( 24) SS BOND : angle 1.48493 ( 48) covalent geometry : bond 0.00589 (17505) covalent geometry : angle 0.69354 (23721) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 228 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 MET cc_start: 0.8155 (ttm) cc_final: 0.7491 (ttm) REVERT: A 456 ARG cc_start: 0.7725 (mtt180) cc_final: 0.7015 (mtm110) REVERT: B 84 TRP cc_start: 0.8053 (OUTLIER) cc_final: 0.7222 (m-10) REVERT: B 176 MET cc_start: 0.8564 (ttm) cc_final: 0.8243 (ttm) REVERT: C 151 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8172 (mmt) REVERT: D 3 GLN cc_start: 0.8328 (mt0) cc_final: 0.8030 (tt0) REVERT: D 105 GLN cc_start: 0.7576 (mp10) cc_final: 0.6883 (pm20) REVERT: E 46 GLU cc_start: 0.7604 (tt0) cc_final: 0.6285 (pm20) REVERT: E 76 ASN cc_start: 0.6658 (m-40) cc_final: 0.6363 (m-40) REVERT: F 103 ARG cc_start: 0.8522 (ttm110) cc_final: 0.8092 (mtt90) REVERT: G 61 ARG cc_start: 0.6504 (ptp90) cc_final: 0.5940 (ptt-90) REVERT: H 105 GLN cc_start: 0.7667 (mp10) cc_final: 0.6958 (pm20) REVERT: L 103 ARG cc_start: 0.8370 (ttm110) cc_final: 0.7989 (mtt90) outliers start: 50 outliers final: 37 residues processed: 262 average time/residue: 0.3132 time to fit residues: 122.6179 Evaluate side-chains 257 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 218 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 242 THR 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 25 SER Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 62 optimal weight: 1.9990 chunk 195 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.170243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.143505 restraints weight = 21944.288| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.98 r_work: 0.3642 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17544 Z= 0.152 Angle : 0.606 12.804 23814 Z= 0.310 Chirality : 0.044 0.196 2589 Planarity : 0.004 0.038 3057 Dihedral : 5.303 36.604 2649 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.15 % Allowed : 13.15 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.17), residues: 2118 helix: 1.56 (0.27), residues: 345 sheet: -0.55 (0.21), residues: 555 loop : -0.90 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 47 HIS 0.007 0.001 HIS C 18 PHE 0.015 0.002 PHE B 439 TYR 0.018 0.002 TYR D 50 ARG 0.004 0.000 ARG A 137 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 12) link_NAG-ASN : angle 2.14070 ( 36) link_BETA1-4 : bond 0.00255 ( 3) link_BETA1-4 : angle 1.44239 ( 9) hydrogen bonds : bond 0.03608 ( 663) hydrogen bonds : angle 5.58891 ( 1863) SS BOND : bond 0.00395 ( 24) SS BOND : angle 1.38943 ( 48) covalent geometry : bond 0.00363 (17505) covalent geometry : angle 0.59781 (23721) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 227 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 MET cc_start: 0.8089 (ttm) cc_final: 0.7370 (ttm) REVERT: A 412 LYS cc_start: 0.8420 (tmtt) cc_final: 0.7501 (mtpp) REVERT: A 456 ARG cc_start: 0.7613 (mtt180) cc_final: 0.6922 (mtm110) REVERT: B 176 MET cc_start: 0.8465 (ttm) cc_final: 0.8148 (ttm) REVERT: B 404 ARG cc_start: 0.8516 (mmm160) cc_final: 0.8009 (mtt-85) REVERT: B 478 MET cc_start: 0.7331 (mmm) cc_final: 0.7079 (mmt) REVERT: C 151 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8117 (mmt) REVERT: C 419 ASP cc_start: 0.8456 (m-30) cc_final: 0.8159 (m-30) REVERT: C 453 MET cc_start: 0.7101 (mtm) cc_final: 0.6855 (mtm) REVERT: D 3 GLN cc_start: 0.8277 (mt0) cc_final: 0.8043 (tt0) REVERT: E 46 GLU cc_start: 0.7580 (tt0) cc_final: 0.6336 (pm20) REVERT: E 76 ASN cc_start: 0.6575 (m-40) cc_final: 0.6305 (m-40) REVERT: F 103 ARG cc_start: 0.8485 (ttm110) cc_final: 0.8011 (mtt90) REVERT: G 61 ARG cc_start: 0.6542 (ptp90) cc_final: 0.6009 (ptt-90) REVERT: G 89 GLN cc_start: 0.7159 (tm-30) cc_final: 0.6824 (tm-30) REVERT: G 103 ARG cc_start: 0.8128 (ttm110) cc_final: 0.7782 (mtt90) REVERT: H 105 GLN cc_start: 0.7622 (mp10) cc_final: 0.6957 (pm20) REVERT: L 103 ARG cc_start: 0.8237 (ttm110) cc_final: 0.7948 (mtt90) outliers start: 40 outliers final: 34 residues processed: 255 average time/residue: 0.3146 time to fit residues: 118.4790 Evaluate side-chains 251 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 151 MET 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 37 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 58 optimal weight: 0.6980 chunk 207 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.170685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.143283 restraints weight = 21817.173| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.03 r_work: 0.3603 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17544 Z= 0.170 Angle : 0.626 13.552 23814 Z= 0.319 Chirality : 0.044 0.196 2589 Planarity : 0.004 0.037 3057 Dihedral : 5.284 36.490 2649 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.04 % Allowed : 13.42 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.17), residues: 2118 helix: 1.54 (0.27), residues: 345 sheet: -0.63 (0.21), residues: 558 loop : -0.96 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 47 HIS 0.007 0.001 HIS C 18 PHE 0.015 0.002 PHE C 439 TYR 0.028 0.002 TYR B 105 ARG 0.006 0.000 ARG A 137 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 12) link_NAG-ASN : angle 2.10066 ( 36) link_BETA1-4 : bond 0.00262 ( 3) link_BETA1-4 : angle 1.44208 ( 9) hydrogen bonds : bond 0.03661 ( 663) hydrogen bonds : angle 5.60713 ( 1863) SS BOND : bond 0.00407 ( 24) SS BOND : angle 1.52787 ( 48) covalent geometry : bond 0.00409 (17505) covalent geometry : angle 0.61758 (23721) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 229 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 MET cc_start: 0.8129 (ttm) cc_final: 0.7424 (ttm) REVERT: A 412 LYS cc_start: 0.8492 (tmtt) cc_final: 0.7776 (mtmt) REVERT: A 456 ARG cc_start: 0.7966 (mtt180) cc_final: 0.7087 (mtm110) REVERT: B 176 MET cc_start: 0.8494 (ttm) cc_final: 0.8160 (ttm) REVERT: B 404 ARG cc_start: 0.8542 (mmm160) cc_final: 0.8020 (mtt-85) REVERT: B 478 MET cc_start: 0.7226 (mmm) cc_final: 0.6973 (mmt) REVERT: C 151 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8130 (mmt) REVERT: C 419 ASP cc_start: 0.8507 (m-30) cc_final: 0.8211 (m-30) REVERT: D 3 GLN cc_start: 0.8316 (mt0) cc_final: 0.8020 (tt0) REVERT: E 46 GLU cc_start: 0.7564 (tt0) cc_final: 0.6236 (pm20) REVERT: E 76 ASN cc_start: 0.6591 (m-40) cc_final: 0.6316 (m-40) REVERT: F 100 GLN cc_start: 0.7412 (mp10) cc_final: 0.7188 (pt0) REVERT: F 103 ARG cc_start: 0.8491 (ttm110) cc_final: 0.8003 (mtt90) REVERT: G 61 ARG cc_start: 0.6489 (ptp90) cc_final: 0.5942 (ptt-90) REVERT: G 82 ASP cc_start: 0.7893 (m-30) cc_final: 0.7451 (m-30) REVERT: G 89 GLN cc_start: 0.7230 (tm-30) cc_final: 0.6941 (tm-30) REVERT: G 103 ARG cc_start: 0.8205 (ttm110) cc_final: 0.7845 (mtt90) REVERT: H 105 GLN cc_start: 0.7677 (mp10) cc_final: 0.6964 (pm20) REVERT: L 103 ARG cc_start: 0.8286 (ttm110) cc_final: 0.7982 (mtt90) outliers start: 38 outliers final: 35 residues processed: 255 average time/residue: 0.3179 time to fit residues: 119.6845 Evaluate side-chains 257 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 221 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 485 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 151 MET 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 25 SER Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 156 optimal weight: 0.0010 chunk 177 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 68 optimal weight: 0.1980 chunk 113 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.172025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.145214 restraints weight = 21659.059| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.98 r_work: 0.3666 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17544 Z= 0.125 Angle : 0.588 14.853 23814 Z= 0.298 Chirality : 0.043 0.194 2589 Planarity : 0.004 0.038 3057 Dihedral : 5.093 35.196 2649 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.99 % Allowed : 13.42 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.18), residues: 2118 helix: 1.65 (0.27), residues: 345 sheet: -0.49 (0.22), residues: 558 loop : -0.91 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 47 HIS 0.005 0.001 HIS C 18 PHE 0.014 0.001 PHE C 439 TYR 0.028 0.001 TYR B 105 ARG 0.004 0.000 ARG A 137 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 12) link_NAG-ASN : angle 1.94020 ( 36) link_BETA1-4 : bond 0.00284 ( 3) link_BETA1-4 : angle 1.47453 ( 9) hydrogen bonds : bond 0.03495 ( 663) hydrogen bonds : angle 5.44184 ( 1863) SS BOND : bond 0.00287 ( 24) SS BOND : angle 1.42862 ( 48) covalent geometry : bond 0.00293 (17505) covalent geometry : angle 0.58006 (23721) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9208.03 seconds wall clock time: 160 minutes 18.26 seconds (9618.26 seconds total)