Starting phenix.real_space_refine on Thu Jul 31 20:08:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tp3_41465/07_2025/8tp3_41465.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tp3_41465/07_2025/8tp3_41465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tp3_41465/07_2025/8tp3_41465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tp3_41465/07_2025/8tp3_41465.map" model { file = "/net/cci-nas-00/data/ceres_data/8tp3_41465/07_2025/8tp3_41465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tp3_41465/07_2025/8tp3_41465.cif" } resolution = 3.6 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= 0.026 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 59 5.16 5 C 8613 2.51 5 N 2322 2.21 5 O 2697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13691 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2530 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "B" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1377 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "C" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2530 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "D" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1328 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 1, 'TRANS': 161} Chain: "G" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2530 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "I" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1377 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 946 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "L" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 796 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Chain: "E" 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: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 8.55, per 1000 atoms: 0.62 Number of scatterers: 13691 At special positions: 0 Unit cell: (98.9, 96.6, 179.4, 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 59 16.00 O 2697 8.00 N 2322 7.00 C 8613 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " 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 B 144 " - pdb=" SG CYS B 148 " distance=2.05 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=2.06 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.06 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.02 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS G 14 " - pdb=" SG CYS I 137 " distance=2.02 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS G 277 " distance=2.04 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 76 " distance=2.02 Simple disulfide: pdb=" SG CYS G 97 " - pdb=" SG CYS G 139 " distance=2.04 Simple disulfide: pdb=" SG CYS G 281 " - pdb=" SG CYS G 305 " distance=2.02 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 148 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 401 " - " ASN A 21 " " NAG A 402 " - " ASN A 33 " " NAG A 403 " - " ASN A 63 " " NAG A 404 " - " ASN A 129 " " NAG C 401 " - " ASN C 21 " " NAG C 402 " - " ASN C 33 " " NAG C 403 " - " ASN C 63 " " NAG C 404 " - " ASN C 129 " " NAG C 405 " - " ASN C 163 " " NAG E 1 " - " ASN A 95 " " NAG F 1 " - " ASN C 95 " " NAG G 401 " - " ASN G 21 " " NAG G 402 " - " ASN G 33 " " NAG G 403 " - " ASN G 63 " " NAG G 404 " - " ASN G 129 " " NAG J 1 " - " ASN G 95 " Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 1.6 seconds 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3128 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 38 sheets defined 25.8% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.896A pdb=" N GLU A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LEU A 78 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 125 through 127 removed outlier: 4.216A pdb=" N TRP A 127 " --> pdb=" O LYS A 125A" (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'B' and resid 37 through 58 Processing helix chain 'B' and resid 74 through 127 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 158 through 161 Processing helix chain 'B' and resid 162 through 170 Processing helix chain 'C' and resid 53 through 56 Processing helix chain 'C' and resid 65 through 70 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.929A pdb=" N GLU C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU C 78 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 114 Processing helix chain 'C' and resid 125 through 127 removed outlier: 4.221A pdb=" N TRP C 127 " --> pdb=" O LYS C 125A" (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'D' and resid 37 through 58 Processing helix chain 'D' and resid 74 through 127 Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 158 through 161 Processing helix chain 'D' and resid 162 through 170 Processing helix chain 'G' and resid 65 through 72 Processing helix chain 'G' and resid 73 through 80 removed outlier: 3.991A pdb=" N GLU G 77 " --> pdb=" O PRO G 74 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU G 78 " --> pdb=" O GLU G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 114 removed outlier: 4.104A pdb=" N SER G 114 " --> pdb=" O GLU G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 127 removed outlier: 4.697A pdb=" N TRP G 127 " --> pdb=" O LYS G 125A" (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 196 Processing helix chain 'I' and resid 37 through 58 Processing helix chain 'I' and resid 74 through 127 Processing helix chain 'I' and resid 145 through 154 Processing helix chain 'I' and resid 158 through 161 Processing helix chain 'I' and resid 162 through 170 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 36 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: 6.339A pdb=" N LEU A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.630A 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 60 removed outlier: 6.471A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE A 87 " --> pdb=" O ILE 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 115 through 122 removed outlier: 6.587A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 115 through 122 removed outlier: 6.587A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.661A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 288 removed outlier: 3.991A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 31 through 36 Processing sheet with id=AB4, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AB5, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.332A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE C 87 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 115 through 122 removed outlier: 6.162A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 115 through 122 removed outlier: 6.162A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 144 through 146 removed outlier: 4.719A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC3, first strand: chain 'C' and resid 286 through 288 removed outlier: 3.908A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 31 through 36 Processing sheet with id=AC5, first strand: chain 'G' and resid 25 through 26 Processing sheet with id=AC6, first strand: chain 'G' and resid 39 through 41 Processing sheet with id=AC7, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AC8, first strand: chain 'G' and resid 51 through 54 removed outlier: 6.353A pdb=" N LEU G 51 " --> pdb=" O ASP G 275 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N CYS G 277 " --> pdb=" O LEU G 51 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 59 through 62 removed outlier: 6.162A pdb=" N LEU G 59 " --> pdb=" O VAL G 88 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE G 87 " --> pdb=" O ILE G 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'G' and resid 115 through 122 removed outlier: 7.218A pdb=" N SER G 261 " --> pdb=" O SER G 116 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE G 118 " --> pdb=" O ALA G 259 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA G 259 " --> pdb=" O PHE G 118 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ARG G 120 " --> pdb=" O ALA G 257 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA G 257 " --> pdb=" O ARG G 120 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU G 175 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU G 179 " --> pdb=" O PRO G 254 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 115 through 122 removed outlier: 7.218A pdb=" N SER G 261 " --> pdb=" O SER G 116 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE G 118 " --> pdb=" O ALA G 259 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA G 259 " --> pdb=" O PHE G 118 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ARG G 120 " --> pdb=" O ALA G 257 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA G 257 " --> pdb=" O ARG G 120 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU G 175 " --> pdb=" O LEU G 260 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 136 through 141 removed outlier: 7.266A pdb=" N SER G 138 " --> pdb=" O LYS G 144 " (cutoff:3.500A) removed outlier: 10.016A pdb=" N LYS G 144 " --> pdb=" O SER G 138 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 164 through 169 Processing sheet with id=AD5, first strand: chain 'G' and resid 286 through 288 removed outlier: 3.842A pdb=" N CYS G 281 " --> pdb=" O ILE G 288 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'H' and resid 56 through 59 removed outlier: 5.493A pdb=" N TYR H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ARG H 38 " --> pdb=" O TYR H 47 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N TYR H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 56 through 59 removed outlier: 5.493A pdb=" N TYR H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ARG H 38 " --> pdb=" O TYR H 47 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N TYR H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AE1, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.948A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.948A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) 613 hydrogen bonds defined for protein. 1650 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.10 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 3995 1.33 - 1.47: 4264 1.47 - 1.61: 5680 1.61 - 1.75: 8 1.75 - 1.89: 73 Bond restraints: 14020 Sorted by residual: bond pdb=" CB HIS H 52 " pdb=" CG HIS H 52 " ideal model delta sigma weight residual 1.497 1.400 0.097 1.40e-02 5.10e+03 4.79e+01 bond pdb=" CB HIS G 47 " pdb=" CG HIS G 47 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.13e+01 bond pdb=" N CYS D 137 " pdb=" CA CYS D 137 " ideal model delta sigma weight residual 1.458 1.522 -0.065 1.19e-02 7.06e+03 2.95e+01 bond pdb=" CB HIS A 18 " pdb=" CG HIS A 18 " ideal model delta sigma weight residual 1.497 1.423 0.074 1.40e-02 5.10e+03 2.76e+01 bond pdb=" CG PHE D 9 " pdb=" CD1 PHE D 9 " ideal model delta sigma weight residual 1.384 1.493 -0.109 2.10e-02 2.27e+03 2.67e+01 ... (remaining 14015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 16958 2.66 - 5.32: 1843 5.32 - 7.98: 210 7.98 - 10.64: 16 10.64 - 13.30: 5 Bond angle restraints: 19032 Sorted by residual: angle pdb=" C HIS A 184 " pdb=" N PRO A 185 " pdb=" CA PRO A 185 " ideal model delta sigma weight residual 119.66 126.54 -6.88 7.30e-01 1.88e+00 8.88e+01 angle pdb=" C HIS G 184 " pdb=" N PRO G 185 " pdb=" CA PRO G 185 " ideal model delta sigma weight residual 119.66 126.33 -6.67 7.30e-01 1.88e+00 8.35e+01 angle pdb=" C ILE A 323 " pdb=" N PRO A 324 " pdb=" CA PRO A 324 " ideal model delta sigma weight residual 120.31 127.58 -7.27 9.80e-01 1.04e+00 5.50e+01 angle pdb=" N LYS A 32 " pdb=" CA LYS A 32 " pdb=" C LYS A 32 " ideal model delta sigma weight residual 111.82 120.16 -8.34 1.16e+00 7.43e-01 5.17e+01 angle pdb=" C CYS C 305 " pdb=" N PRO C 306 " pdb=" CA PRO C 306 " ideal model delta sigma weight residual 119.78 127.11 -7.33 1.03e+00 9.43e-01 5.07e+01 ... (remaining 19027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.02: 8348 21.02 - 42.05: 168 42.05 - 63.07: 51 63.07 - 84.09: 16 84.09 - 105.12: 7 Dihedral angle restraints: 8590 sinusoidal: 3687 harmonic: 4903 Sorted by residual: dihedral pdb=" CB CYS C 14 " pdb=" SG CYS C 14 " pdb=" SG CYS D 137 " pdb=" CB CYS D 137 " ideal model delta sinusoidal sigma weight residual -86.00 -9.50 -76.50 1 1.00e+01 1.00e-02 7.36e+01 dihedral pdb=" CB CYS D 144 " pdb=" SG CYS D 144 " pdb=" SG CYS D 148 " pdb=" CB CYS D 148 " ideal model delta sinusoidal sigma weight residual 93.00 148.33 -55.33 1 1.00e+01 1.00e-02 4.14e+01 dihedral pdb=" CB CYS C 64 " pdb=" SG CYS C 64 " pdb=" SG CYS C 76 " pdb=" CB CYS C 76 " ideal model delta sinusoidal sigma weight residual -86.00 -45.01 -40.99 1 1.00e+01 1.00e-02 2.35e+01 ... (remaining 8587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1526 0.104 - 0.208: 454 0.208 - 0.312: 71 0.312 - 0.416: 30 0.416 - 0.520: 14 Chirality restraints: 2095 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.29e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.67e+01 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 -2.56 0.16 2.00e-02 2.50e+03 6.24e+01 ... (remaining 2092 not shown) Planarity restraints: 2467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 401 " -0.122 2.00e-02 2.50e+03 1.00e-01 1.25e+02 pdb=" C7 NAG A 401 " 0.033 2.00e-02 2.50e+03 pdb=" C8 NAG A 401 " -0.091 2.00e-02 2.50e+03 pdb=" N2 NAG A 401 " 0.159 2.00e-02 2.50e+03 pdb=" O7 NAG A 401 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 401 " 0.096 2.00e-02 2.50e+03 8.10e-02 8.21e+01 pdb=" C7 NAG G 401 " -0.021 2.00e-02 2.50e+03 pdb=" C8 NAG G 401 " -0.025 2.00e-02 2.50e+03 pdb=" N2 NAG G 401 " -0.128 2.00e-02 2.50e+03 pdb=" O7 NAG G 401 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 95 " 0.075 2.00e-02 2.50e+03 7.74e-02 7.49e+01 pdb=" CG ASN C 95 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN C 95 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN C 95 " -0.119 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.093 2.00e-02 2.50e+03 ... (remaining 2464 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 4616 2.85 - 3.36: 12475 3.36 - 3.87: 24009 3.87 - 4.39: 28160 4.39 - 4.90: 45794 Nonbonded interactions: 115054 Sorted by model distance: nonbonded pdb=" NZ LYS D 83 " pdb=" OD1 ASP I 85 " model vdw 2.336 3.120 nonbonded pdb=" NZ LYS B 83 " pdb=" OD1 ASP D 85 " model vdw 2.342 3.120 nonbonded pdb=" OD1 ASP B 85 " pdb=" NZ LYS I 83 " model vdw 2.350 3.120 nonbonded pdb=" N ASP B 19 " pdb=" OD1 ASP B 19 " model vdw 2.380 3.120 nonbonded pdb=" N ASN H 76 " pdb=" N GLN H 77 " model vdw 2.396 2.560 ... (remaining 115049 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 11 through 325 or resid 401 through 404)) selection = chain 'G' } ncs_group { reference = (chain 'B' and resid 9 through 171) selection = chain 'D' selection = (chain 'I' and resid 9 through 171) } ncs_group { reference = chain 'E' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 31.950 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.050 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 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 0.121 14060 Z= 1.068 Angle : 1.759 31.410 19132 Z= 1.160 Chirality : 0.110 0.520 2095 Planarity : 0.009 0.122 2451 Dihedral : 10.547 105.117 5402 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.07 % Allowed : 0.41 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.78 (0.19), residues: 1684 helix: 0.86 (0.24), residues: 358 sheet: 0.89 (0.26), residues: 330 loop : 0.38 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.007 TRP D 21 HIS 0.010 0.003 HIS C 38 PHE 0.052 0.007 PHE H 100J TYR 0.050 0.009 TYR D 157 ARG 0.009 0.001 ARG H 66 Details of bonding type rmsd link_NAG-ASN : bond 0.07259 ( 16) link_NAG-ASN : angle 3.25146 ( 48) link_BETA1-4 : bond 0.06779 ( 4) link_BETA1-4 : angle 4.13060 ( 12) hydrogen bonds : bond 0.16452 ( 574) hydrogen bonds : angle 7.83854 ( 1650) SS BOND : bond 0.01239 ( 20) SS BOND : angle 7.33259 ( 40) covalent geometry : bond 0.01998 (14020) covalent geometry : angle 1.72001 (19032) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 488 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7203 (mmtt) cc_final: 0.6593 (mmmt) REVERT: A 104 ASP cc_start: 0.9064 (m-30) cc_final: 0.8862 (m-30) REVERT: A 274 MET cc_start: 0.7445 (mtt) cc_final: 0.7236 (ttt) REVERT: B 46 ASN cc_start: 0.7856 (m-40) cc_final: 0.7608 (t0) REVERT: B 53 ASN cc_start: 0.6760 (m-40) cc_final: 0.5744 (t0) REVERT: C 82 LYS cc_start: 0.7522 (mmtt) cc_final: 0.6903 (tptp) REVERT: D 11 GLU cc_start: 0.7209 (tt0) cc_final: 0.6938 (pm20) REVERT: D 77 MET cc_start: 0.7521 (ttt) cc_final: 0.7133 (ttm) REVERT: D 142 HIS cc_start: 0.8256 (p90) cc_final: 0.7765 (p90) REVERT: G 75 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6818 (mm-30) REVERT: G 107 GLU cc_start: 0.8307 (tp30) cc_final: 0.8094 (tp30) REVERT: G 148 TYR cc_start: 0.8047 (m-80) cc_final: 0.7523 (m-80) REVERT: G 201 TYR cc_start: 0.7945 (p90) cc_final: 0.7215 (p90) REVERT: G 224 ARG cc_start: 0.8435 (mtp85) cc_final: 0.6353 (mpt180) REVERT: G 256 TYR cc_start: 0.8342 (m-80) cc_final: 0.7913 (m-10) REVERT: I 34 TYR cc_start: 0.5419 (m-80) cc_final: 0.5105 (m-80) REVERT: I 109 ASP cc_start: 0.8289 (m-30) cc_final: 0.7822 (t70) REVERT: H 3 GLN cc_start: 0.7716 (mm-40) cc_final: 0.7479 (mm110) REVERT: H 36 TRP cc_start: 0.7984 (m100) cc_final: 0.7323 (m100) REVERT: H 100 PHE cc_start: 0.7508 (m-80) cc_final: 0.7218 (m-80) outliers start: 1 outliers final: 0 residues processed: 488 average time/residue: 0.2773 time to fit residues: 191.1529 Evaluate side-chains 238 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.0470 chunk 127 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN C 295 GLN C 298 HIS ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 298 HIS ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.164926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.140764 restraints weight = 22156.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.144533 restraints weight = 13010.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.147007 restraints weight = 8942.914| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 14060 Z= 0.190 Angle : 0.755 21.985 19132 Z= 0.394 Chirality : 0.049 0.460 2095 Planarity : 0.005 0.056 2451 Dihedral : 6.918 66.921 2253 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.58 % Allowed : 9.94 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.81 (0.19), residues: 1684 helix: 1.86 (0.26), residues: 361 sheet: 1.18 (0.31), residues: 254 loop : -0.05 (0.17), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 153 HIS 0.010 0.002 HIS A 196 PHE 0.019 0.002 PHE G 118 TYR 0.019 0.002 TYR G 86 ARG 0.006 0.001 ARG C 321 Details of bonding type rmsd link_NAG-ASN : bond 0.00595 ( 16) link_NAG-ASN : angle 4.67273 ( 48) link_BETA1-4 : bond 0.00198 ( 4) link_BETA1-4 : angle 2.67943 ( 12) hydrogen bonds : bond 0.06461 ( 574) hydrogen bonds : angle 5.98068 ( 1650) SS BOND : bond 0.00406 ( 20) SS BOND : angle 1.30175 ( 40) covalent geometry : bond 0.00425 (14020) covalent geometry : angle 0.71450 (19032) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 275 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7221 (mmtt) cc_final: 0.6802 (mmmt) REVERT: A 104 ASP cc_start: 0.8946 (m-30) cc_final: 0.8723 (m-30) REVERT: A 223 VAL cc_start: 0.6451 (m) cc_final: 0.6251 (m) REVERT: A 274 MET cc_start: 0.7250 (mtt) cc_final: 0.6919 (ttt) REVERT: B 17 MET cc_start: 0.7509 (ttt) cc_final: 0.7270 (ttt) REVERT: B 19 ASP cc_start: 0.7567 (p0) cc_final: 0.6774 (t0) REVERT: B 53 ASN cc_start: 0.5938 (m-40) cc_final: 0.5520 (t0) REVERT: B 128 ASN cc_start: 0.7509 (m-40) cc_final: 0.7051 (t0) REVERT: B 141 TYR cc_start: 0.6249 (m-80) cc_final: 0.5328 (m-80) REVERT: C 82 LYS cc_start: 0.7249 (mmtt) cc_final: 0.7011 (tptp) REVERT: C 226 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7562 (mm-40) REVERT: D 142 HIS cc_start: 0.8252 (p90) cc_final: 0.7757 (p90) REVERT: G 45 ASP cc_start: 0.7983 (p0) cc_final: 0.7679 (p0) REVERT: G 107 GLU cc_start: 0.7708 (tp30) cc_final: 0.7370 (tp30) REVERT: G 224 ARG cc_start: 0.8220 (mtp85) cc_final: 0.6254 (mtt180) REVERT: I 109 ASP cc_start: 0.7897 (m-30) cc_final: 0.7377 (t70) REVERT: H 36 TRP cc_start: 0.8226 (m100) cc_final: 0.7419 (m100) REVERT: L 1 GLU cc_start: 0.5409 (pp20) cc_final: 0.5035 (mp0) REVERT: L 48 ILE cc_start: 0.7942 (mp) cc_final: 0.7733 (mt) REVERT: L 89 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.6257 (tt0) REVERT: L 100 GLN cc_start: 0.7473 (pm20) cc_final: 0.7194 (pm20) outliers start: 53 outliers final: 26 residues processed: 312 average time/residue: 0.2541 time to fit residues: 115.8233 Evaluate side-chains 248 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 221 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 92 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 128 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 HIS C 141 HIS C 190 ASN C 282 GLN C 295 GLN D 27 GLN G 208 HIS I 125 GLN I 129 ASN ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.158899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.135391 restraints weight = 22090.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.138572 restraints weight = 13924.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.140702 restraints weight = 10073.800| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 14060 Z= 0.280 Angle : 0.793 21.110 19132 Z= 0.409 Chirality : 0.052 0.400 2095 Planarity : 0.006 0.061 2451 Dihedral : 6.234 54.597 2253 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.60 % Allowed : 12.10 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.19), residues: 1684 helix: 1.71 (0.26), residues: 363 sheet: 0.60 (0.32), residues: 247 loop : -0.43 (0.17), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 153 HIS 0.009 0.002 HIS G 183 PHE 0.032 0.003 PHE G 118 TYR 0.022 0.002 TYR L 91 ARG 0.009 0.001 ARG B 170 Details of bonding type rmsd link_NAG-ASN : bond 0.01054 ( 16) link_NAG-ASN : angle 4.52309 ( 48) link_BETA1-4 : bond 0.00260 ( 4) link_BETA1-4 : angle 2.12289 ( 12) hydrogen bonds : bond 0.05941 ( 574) hydrogen bonds : angle 5.78331 ( 1650) SS BOND : bond 0.00540 ( 20) SS BOND : angle 1.40335 ( 40) covalent geometry : bond 0.00646 (14020) covalent geometry : angle 0.75774 (19032) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 247 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.7802 (t0) cc_final: 0.7523 (t0) REVERT: A 32 LYS cc_start: 0.8500 (mttp) cc_final: 0.7902 (mmmt) REVERT: B 125 GLN cc_start: 0.7479 (mm-40) cc_final: 0.6978 (tt0) REVERT: B 141 TYR cc_start: 0.6407 (m-80) cc_final: 0.5631 (m-80) REVERT: B 170 ARG cc_start: 0.7056 (ttm110) cc_final: 0.6628 (ttm110) REVERT: D 45 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7688 (mp) REVERT: D 125 GLN cc_start: 0.8280 (tp40) cc_final: 0.7547 (tp-100) REVERT: D 142 HIS cc_start: 0.8341 (p90) cc_final: 0.7815 (p90) REVERT: D 162 TYR cc_start: 0.8323 (m-80) cc_final: 0.8066 (m-80) REVERT: G 224 ARG cc_start: 0.8098 (mtp85) cc_final: 0.6425 (mtt180) REVERT: G 314 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.6118 (mm) REVERT: G 320 LEU cc_start: 0.8665 (mp) cc_final: 0.8410 (mt) REVERT: I 55 VAL cc_start: 0.8260 (t) cc_final: 0.7929 (t) REVERT: I 109 ASP cc_start: 0.8034 (m-30) cc_final: 0.7706 (t70) REVERT: H 36 TRP cc_start: 0.8476 (m100) cc_final: 0.7817 (m100) REVERT: L 89 GLN cc_start: 0.7078 (OUTLIER) cc_final: 0.6640 (tt0) outliers start: 68 outliers final: 50 residues processed: 292 average time/residue: 0.2535 time to fit residues: 108.6089 Evaluate side-chains 257 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 204 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 129 ASN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 92 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 129 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 152 optimal weight: 0.0040 chunk 99 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN ** C 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.167531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.143794 restraints weight = 22241.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.147406 restraints weight = 13176.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.149847 restraints weight = 9157.716| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 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 : 0.004 0.046 14060 Z= 0.179 Angle : 0.678 20.871 19132 Z= 0.345 Chirality : 0.046 0.405 2095 Planarity : 0.005 0.055 2451 Dihedral : 5.704 55.331 2253 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.92 % Allowed : 14.87 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.19), residues: 1684 helix: 1.93 (0.26), residues: 363 sheet: 0.48 (0.32), residues: 246 loop : -0.51 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 96 HIS 0.005 0.001 HIS I 142 PHE 0.023 0.002 PHE G 118 TYR 0.022 0.002 TYR C 201 ARG 0.006 0.001 ARG D 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00719 ( 16) link_NAG-ASN : angle 4.17653 ( 48) link_BETA1-4 : bond 0.00252 ( 4) link_BETA1-4 : angle 1.83290 ( 12) hydrogen bonds : bond 0.05308 ( 574) hydrogen bonds : angle 5.52985 ( 1650) SS BOND : bond 0.00836 ( 20) SS BOND : angle 1.12831 ( 40) covalent geometry : bond 0.00411 (14020) covalent geometry : angle 0.64236 (19032) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 223 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ILE cc_start: 0.6389 (mt) cc_final: 0.6174 (mt) REVERT: A 27 ASP cc_start: 0.7758 (t0) cc_final: 0.7516 (t0) REVERT: A 32 LYS cc_start: 0.8604 (mttp) cc_final: 0.7207 (mmmt) REVERT: B 125 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7091 (tt0) REVERT: B 141 TYR cc_start: 0.6415 (m-80) cc_final: 0.5556 (m-80) REVERT: C 225 ASP cc_start: 0.7422 (t0) cc_final: 0.7104 (t0) REVERT: C 226 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7564 (mm-40) REVERT: D 58 LYS cc_start: 0.7295 (mmmt) cc_final: 0.6965 (mmtt) REVERT: D 125 GLN cc_start: 0.8232 (tp40) cc_final: 0.7568 (tp-100) REVERT: D 142 HIS cc_start: 0.8444 (p90) cc_final: 0.7874 (p90) REVERT: G 148 TYR cc_start: 0.7960 (m-80) cc_final: 0.7507 (m-80) REVERT: G 224 ARG cc_start: 0.8100 (mtp85) cc_final: 0.6428 (mtt180) REVERT: G 314 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.5982 (mm) REVERT: G 320 LEU cc_start: 0.8660 (mp) cc_final: 0.8345 (mt) REVERT: I 109 ASP cc_start: 0.8047 (m-30) cc_final: 0.7730 (t70) REVERT: H 36 TRP cc_start: 0.8358 (m100) cc_final: 0.7602 (m100) REVERT: H 100 PHE cc_start: 0.7090 (m-80) cc_final: 0.6283 (m-80) REVERT: L 89 GLN cc_start: 0.7017 (OUTLIER) cc_final: 0.6532 (tt0) outliers start: 58 outliers final: 43 residues processed: 260 average time/residue: 0.2376 time to fit residues: 92.3186 Evaluate side-chains 251 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 206 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 92 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 89 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 147 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 27 optimal weight: 0.0970 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 HIS D 43 ASN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.164540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.140330 restraints weight = 22602.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.143898 restraints weight = 13511.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.146246 restraints weight = 9439.473| |-----------------------------------------------------------------------------| r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 14060 Z= 0.204 Angle : 0.684 20.662 19132 Z= 0.347 Chirality : 0.047 0.396 2095 Planarity : 0.005 0.057 2451 Dihedral : 5.597 55.359 2253 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 5.14 % Allowed : 14.00 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.05 (0.19), residues: 1684 helix: 1.86 (0.27), residues: 363 sheet: 0.22 (0.31), residues: 260 loop : -0.69 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 103 HIS 0.005 0.001 HIS G 183 PHE 0.026 0.002 PHE G 118 TYR 0.026 0.002 TYR B 119 ARG 0.011 0.001 ARG B 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00728 ( 16) link_NAG-ASN : angle 4.05942 ( 48) link_BETA1-4 : bond 0.00240 ( 4) link_BETA1-4 : angle 1.72554 ( 12) hydrogen bonds : bond 0.05143 ( 574) hydrogen bonds : angle 5.48664 ( 1650) SS BOND : bond 0.00460 ( 20) SS BOND : angle 1.10064 ( 40) covalent geometry : bond 0.00477 (14020) covalent geometry : angle 0.65105 (19032) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 222 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.7963 (t0) cc_final: 0.7676 (t0) REVERT: A 32 LYS cc_start: 0.8252 (mttp) cc_final: 0.7425 (mmmt) REVERT: B 59 MET cc_start: 0.7203 (tpp) cc_final: 0.6850 (tpp) REVERT: B 125 GLN cc_start: 0.7588 (mm-40) cc_final: 0.7137 (tt0) REVERT: B 141 TYR cc_start: 0.6520 (m-80) cc_final: 0.5538 (m-80) REVERT: C 225 ASP cc_start: 0.7339 (t0) cc_final: 0.7108 (t0) REVERT: C 226 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7556 (mm110) REVERT: D 45 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7543 (mp) REVERT: D 58 LYS cc_start: 0.7314 (mmmt) cc_final: 0.7108 (mmtt) REVERT: D 125 GLN cc_start: 0.8287 (tp40) cc_final: 0.7610 (tp-100) REVERT: D 143 LYS cc_start: 0.8080 (mmmt) cc_final: 0.7865 (mmmt) REVERT: G 179 LEU cc_start: 0.5602 (OUTLIER) cc_final: 0.5233 (mt) REVERT: G 224 ARG cc_start: 0.8236 (mtp85) cc_final: 0.6519 (mtt180) REVERT: G 245 PHE cc_start: 0.6169 (m-80) cc_final: 0.5797 (m-10) REVERT: G 314 LEU cc_start: 0.6543 (OUTLIER) cc_final: 0.6077 (mm) REVERT: I 109 ASP cc_start: 0.8088 (m-30) cc_final: 0.7845 (t70) REVERT: H 77 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7385 (pp30) REVERT: H 100 PHE cc_start: 0.7063 (m-80) cc_final: 0.6193 (m-80) REVERT: L 89 GLN cc_start: 0.7055 (OUTLIER) cc_final: 0.6510 (tt0) outliers start: 76 outliers final: 60 residues processed: 269 average time/residue: 0.2356 time to fit residues: 93.6834 Evaluate side-chains 272 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 207 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 92 ASN Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN ** C 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.159396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.135530 restraints weight = 22201.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.138817 restraints weight = 13764.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.141000 restraints weight = 9792.930| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14060 Z= 0.211 Angle : 0.704 20.724 19132 Z= 0.356 Chirality : 0.048 0.398 2095 Planarity : 0.005 0.058 2451 Dihedral : 5.666 55.267 2253 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.07 % Allowed : 15.08 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.11 (0.20), residues: 1684 helix: 1.80 (0.27), residues: 363 sheet: -0.03 (0.31), residues: 272 loop : -0.78 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 103 HIS 0.006 0.001 HIS B 26 PHE 0.027 0.002 PHE G 118 TYR 0.026 0.002 TYR B 119 ARG 0.010 0.001 ARG B 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00815 ( 16) link_NAG-ASN : angle 4.64418 ( 48) link_BETA1-4 : bond 0.00253 ( 4) link_BETA1-4 : angle 1.72335 ( 12) hydrogen bonds : bond 0.05110 ( 574) hydrogen bonds : angle 5.49905 ( 1650) SS BOND : bond 0.00503 ( 20) SS BOND : angle 1.27853 ( 40) covalent geometry : bond 0.00493 (14020) covalent geometry : angle 0.66170 (19032) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 220 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8009 (t0) cc_final: 0.7663 (t0) REVERT: A 32 LYS cc_start: 0.8258 (mttp) cc_final: 0.7468 (mmmt) REVERT: B 125 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7287 (tt0) REVERT: B 137 CYS cc_start: 0.5294 (m) cc_final: 0.4892 (m) REVERT: B 141 TYR cc_start: 0.6554 (m-80) cc_final: 0.5658 (m-80) REVERT: C 225 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6952 (t0) REVERT: D 45 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7740 (mp) REVERT: D 119 TYR cc_start: 0.8449 (t80) cc_final: 0.8105 (t80) REVERT: D 125 GLN cc_start: 0.8274 (tp40) cc_final: 0.7923 (tp40) REVERT: D 142 HIS cc_start: 0.7979 (p90) cc_final: 0.7664 (p90) REVERT: G 179 LEU cc_start: 0.5709 (OUTLIER) cc_final: 0.5434 (mt) REVERT: G 187 ASN cc_start: 0.7261 (p0) cc_final: 0.7049 (p0) REVERT: G 224 ARG cc_start: 0.8238 (mtp85) cc_final: 0.6575 (mtt180) REVERT: G 314 LEU cc_start: 0.6480 (OUTLIER) cc_final: 0.6025 (mm) REVERT: I 109 ASP cc_start: 0.8166 (m-30) cc_final: 0.7639 (t0) REVERT: H 100 PHE cc_start: 0.6852 (m-80) cc_final: 0.6112 (m-80) REVERT: L 89 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.6514 (tt0) outliers start: 75 outliers final: 59 residues processed: 269 average time/residue: 0.2366 time to fit residues: 96.1395 Evaluate side-chains 265 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 201 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 92 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 3 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 51 optimal weight: 0.3980 chunk 78 optimal weight: 3.9990 chunk 162 optimal weight: 0.0970 chunk 105 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN C 226 GLN C 282 GLN ** C 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN I 125 GLN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 ASN ** 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 = 0.4179 r_free = 0.4179 target = 0.160956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.137502 restraints weight = 21975.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.140663 restraints weight = 13729.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.142912 restraints weight = 9844.450| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14060 Z= 0.137 Angle : 0.646 20.225 19132 Z= 0.323 Chirality : 0.045 0.391 2095 Planarity : 0.004 0.051 2451 Dihedral : 5.423 55.178 2253 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.12 % Allowed : 16.36 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.04 (0.20), residues: 1684 helix: 2.01 (0.27), residues: 363 sheet: 0.06 (0.31), residues: 265 loop : -0.72 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 36 HIS 0.004 0.001 HIS C 18 PHE 0.020 0.002 PHE G 118 TYR 0.030 0.002 TYR D 162 ARG 0.010 0.001 ARG B 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00721 ( 16) link_NAG-ASN : angle 4.28743 ( 48) link_BETA1-4 : bond 0.00329 ( 4) link_BETA1-4 : angle 1.64470 ( 12) hydrogen bonds : bond 0.04763 ( 574) hydrogen bonds : angle 5.33017 ( 1650) SS BOND : bond 0.00330 ( 20) SS BOND : angle 1.13106 ( 40) covalent geometry : bond 0.00313 (14020) covalent geometry : angle 0.60745 (19032) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 216 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.7964 (t0) cc_final: 0.7655 (t0) REVERT: A 32 LYS cc_start: 0.8232 (mttp) cc_final: 0.7472 (mmmt) REVERT: B 118 LEU cc_start: 0.8296 (tp) cc_final: 0.8018 (tp) REVERT: B 125 GLN cc_start: 0.7611 (mm-40) cc_final: 0.7315 (tt0) REVERT: B 137 CYS cc_start: 0.5227 (m) cc_final: 0.4827 (m) REVERT: B 141 TYR cc_start: 0.6559 (m-80) cc_final: 0.5633 (m-80) REVERT: C 225 ASP cc_start: 0.7179 (OUTLIER) cc_final: 0.6710 (t0) REVERT: D 45 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7671 (mp) REVERT: D 119 TYR cc_start: 0.8473 (t80) cc_final: 0.8165 (t80) REVERT: D 125 GLN cc_start: 0.8191 (tp-100) cc_final: 0.7900 (tp40) REVERT: D 142 HIS cc_start: 0.7963 (p90) cc_final: 0.7612 (p90) REVERT: G 175 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7261 (mp0) REVERT: G 179 LEU cc_start: 0.5411 (OUTLIER) cc_final: 0.5132 (mt) REVERT: G 195 TYR cc_start: 0.8095 (m-80) cc_final: 0.7883 (m-10) REVERT: G 224 ARG cc_start: 0.8210 (mtp85) cc_final: 0.6456 (mtt180) REVERT: G 314 LEU cc_start: 0.6292 (OUTLIER) cc_final: 0.5856 (mm) REVERT: I 109 ASP cc_start: 0.7932 (m-30) cc_final: 0.7664 (t0) REVERT: H 45 LEU cc_start: 0.7612 (mm) cc_final: 0.7355 (mm) REVERT: H 100 PHE cc_start: 0.6691 (m-80) cc_final: 0.5969 (m-80) REVERT: L 89 GLN cc_start: 0.7072 (OUTLIER) cc_final: 0.6665 (tt0) outliers start: 61 outliers final: 48 residues processed: 259 average time/residue: 0.2246 time to fit residues: 89.0239 Evaluate side-chains 254 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 200 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 175 GLU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 92 ASN Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 67 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 164 optimal weight: 20.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN ** C 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN D 60 ASN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.155581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.131951 restraints weight = 22296.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.134885 restraints weight = 14261.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.137010 restraints weight = 10445.256| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 14060 Z= 0.272 Angle : 0.755 20.708 19132 Z= 0.382 Chirality : 0.049 0.395 2095 Planarity : 0.005 0.062 2451 Dihedral : 5.826 54.971 2253 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.80 % Allowed : 16.43 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.20), residues: 1684 helix: 1.57 (0.26), residues: 363 sheet: -0.23 (0.29), residues: 301 loop : -0.92 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 36 HIS 0.007 0.002 HIS B 26 PHE 0.033 0.003 PHE G 118 TYR 0.032 0.003 TYR B 119 ARG 0.012 0.001 ARG B 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00790 ( 16) link_NAG-ASN : angle 4.27624 ( 48) link_BETA1-4 : bond 0.00301 ( 4) link_BETA1-4 : angle 1.99810 ( 12) hydrogen bonds : bond 0.05311 ( 574) hydrogen bonds : angle 5.67187 ( 1650) SS BOND : bond 0.00699 ( 20) SS BOND : angle 1.29992 ( 40) covalent geometry : bond 0.00641 (14020) covalent geometry : angle 0.72205 (19032) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 204 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8158 (t0) cc_final: 0.7760 (t0) REVERT: A 32 LYS cc_start: 0.8250 (mttp) cc_final: 0.7902 (mttp) REVERT: B 59 MET cc_start: 0.7115 (tpp) cc_final: 0.6657 (tpp) REVERT: B 116 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.7967 (ttmm) REVERT: B 118 LEU cc_start: 0.8372 (tp) cc_final: 0.8094 (tp) REVERT: B 137 CYS cc_start: 0.5225 (m) cc_final: 0.4839 (m) REVERT: B 141 TYR cc_start: 0.6603 (m-80) cc_final: 0.5665 (m-80) REVERT: C 18 HIS cc_start: 0.7823 (OUTLIER) cc_final: 0.7500 (p-80) REVERT: C 105 TYR cc_start: 0.7374 (t80) cc_final: 0.6971 (t80) REVERT: D 45 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7698 (mp) REVERT: D 125 GLN cc_start: 0.8275 (tp-100) cc_final: 0.7953 (tp40) REVERT: D 168 LEU cc_start: 0.8773 (tp) cc_final: 0.8570 (mt) REVERT: G 32 LYS cc_start: 0.7039 (mmmm) cc_final: 0.6820 (mmtt) REVERT: G 175 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: G 179 LEU cc_start: 0.5671 (OUTLIER) cc_final: 0.5295 (mt) REVERT: G 187 ASN cc_start: 0.7276 (p0) cc_final: 0.7049 (p0) REVERT: G 195 TYR cc_start: 0.8172 (m-80) cc_final: 0.7776 (m-10) REVERT: G 224 ARG cc_start: 0.8286 (mtp85) cc_final: 0.6521 (mtt180) REVERT: G 314 LEU cc_start: 0.6676 (OUTLIER) cc_final: 0.6164 (mm) REVERT: H 100 PHE cc_start: 0.6841 (m-80) cc_final: 0.6154 (m-80) REVERT: L 89 GLN cc_start: 0.7163 (OUTLIER) cc_final: 0.6625 (tt0) outliers start: 71 outliers final: 56 residues processed: 255 average time/residue: 0.2295 time to fit residues: 88.2603 Evaluate side-chains 253 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 190 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 175 GLU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 225 ASP Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 92 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 37 optimal weight: 0.7980 chunk 142 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 141 optimal weight: 0.2980 chunk 115 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN C 282 GLN ** C 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN D 62 GLN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.162635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.138267 restraints weight = 22276.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.141207 restraints weight = 14525.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.143298 restraints weight = 10716.868| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.5649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14060 Z= 0.148 Angle : 0.690 20.166 19132 Z= 0.342 Chirality : 0.047 0.596 2095 Planarity : 0.004 0.061 2451 Dihedral : 5.806 59.005 2253 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.72 % Allowed : 18.26 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.13 (0.20), residues: 1684 helix: 1.90 (0.27), residues: 363 sheet: -0.07 (0.29), residues: 295 loop : -0.85 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 36 HIS 0.006 0.001 HIS C 18 PHE 0.021 0.002 PHE G 118 TYR 0.027 0.002 TYR B 119 ARG 0.009 0.001 ARG B 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00712 ( 16) link_NAG-ASN : angle 4.73997 ( 48) link_BETA1-4 : bond 0.00539 ( 4) link_BETA1-4 : angle 1.71518 ( 12) hydrogen bonds : bond 0.04772 ( 574) hydrogen bonds : angle 5.40337 ( 1650) SS BOND : bond 0.00318 ( 20) SS BOND : angle 1.26389 ( 40) covalent geometry : bond 0.00342 (14020) covalent geometry : angle 0.64587 (19032) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 211 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8101 (t0) cc_final: 0.7686 (t0) REVERT: A 32 LYS cc_start: 0.8354 (mttp) cc_final: 0.8097 (mttp) REVERT: A 323 ILE cc_start: 0.8198 (mp) cc_final: 0.7560 (tt) REVERT: B 59 MET cc_start: 0.6905 (tpp) cc_final: 0.6465 (tpp) REVERT: B 118 LEU cc_start: 0.8283 (tp) cc_final: 0.8035 (tp) REVERT: B 137 CYS cc_start: 0.4900 (m) cc_final: 0.4558 (m) REVERT: B 141 TYR cc_start: 0.6546 (m-80) cc_final: 0.5651 (m-80) REVERT: C 18 HIS cc_start: 0.7709 (OUTLIER) cc_final: 0.7407 (p-80) REVERT: C 105 TYR cc_start: 0.6983 (t80) cc_final: 0.6716 (t80) REVERT: C 225 ASP cc_start: 0.7023 (t0) cc_final: 0.6177 (t0) REVERT: D 45 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7647 (mp) REVERT: D 119 TYR cc_start: 0.8500 (t80) cc_final: 0.8150 (t80) REVERT: D 125 GLN cc_start: 0.8188 (tp-100) cc_final: 0.7915 (tp40) REVERT: D 142 HIS cc_start: 0.8201 (p90) cc_final: 0.7739 (p90) REVERT: D 168 LEU cc_start: 0.8791 (tp) cc_final: 0.8569 (mt) REVERT: G 77 GLU cc_start: 0.6844 (pm20) cc_final: 0.5936 (mm-30) REVERT: G 175 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: G 179 LEU cc_start: 0.5570 (OUTLIER) cc_final: 0.5168 (mt) REVERT: G 187 ASN cc_start: 0.7097 (p0) cc_final: 0.6872 (p0) REVERT: G 195 TYR cc_start: 0.8157 (m-80) cc_final: 0.7853 (m-10) REVERT: G 224 ARG cc_start: 0.8302 (mtp85) cc_final: 0.6608 (mtt180) REVERT: G 245 PHE cc_start: 0.6073 (m-80) cc_final: 0.5749 (m-10) REVERT: G 314 LEU cc_start: 0.6533 (OUTLIER) cc_final: 0.6043 (mm) REVERT: H 45 LEU cc_start: 0.7671 (mm) cc_final: 0.7399 (mm) REVERT: H 100 PHE cc_start: 0.6702 (m-80) cc_final: 0.6357 (m-80) REVERT: L 89 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.6716 (tt0) outliers start: 55 outliers final: 44 residues processed: 251 average time/residue: 0.2226 time to fit residues: 84.8139 Evaluate side-chains 250 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 200 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 175 GLU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 92 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 122 optimal weight: 0.0870 chunk 29 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 115 optimal weight: 0.2980 chunk 54 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 159 optimal weight: 0.0980 chunk 2 optimal weight: 0.7980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 GLN D 60 ASN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 ASN ** 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 = 0.4206 r_free = 0.4206 target = 0.164625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.140535 restraints weight = 22178.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.143619 restraints weight = 14286.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.145798 restraints weight = 10487.341| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14060 Z= 0.127 Angle : 0.652 19.881 19132 Z= 0.322 Chirality : 0.046 0.575 2095 Planarity : 0.004 0.048 2451 Dihedral : 5.480 56.475 2253 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.58 % Allowed : 18.19 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.05 (0.20), residues: 1684 helix: 2.06 (0.27), residues: 363 sheet: -0.08 (0.30), residues: 285 loop : -0.80 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 36 HIS 0.005 0.001 HIS C 18 PHE 0.018 0.002 PHE G 118 TYR 0.025 0.002 TYR B 119 ARG 0.013 0.001 ARG A 310 Details of bonding type rmsd link_NAG-ASN : bond 0.00908 ( 16) link_NAG-ASN : angle 4.49822 ( 48) link_BETA1-4 : bond 0.00408 ( 4) link_BETA1-4 : angle 1.50764 ( 12) hydrogen bonds : bond 0.04461 ( 574) hydrogen bonds : angle 5.25842 ( 1650) SS BOND : bond 0.00336 ( 20) SS BOND : angle 1.04452 ( 40) covalent geometry : bond 0.00291 (14020) covalent geometry : angle 0.61044 (19032) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 217 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8050 (t0) cc_final: 0.7707 (t0) REVERT: A 32 LYS cc_start: 0.8469 (mttp) cc_final: 0.8060 (mppt) REVERT: B 118 LEU cc_start: 0.8298 (tp) cc_final: 0.8093 (tp) REVERT: B 137 CYS cc_start: 0.5024 (m) cc_final: 0.4655 (m) REVERT: B 141 TYR cc_start: 0.6580 (m-80) cc_final: 0.5701 (m-80) REVERT: C 18 HIS cc_start: 0.7618 (OUTLIER) cc_final: 0.7307 (p-80) REVERT: C 105 TYR cc_start: 0.6965 (t80) cc_final: 0.6607 (t80) REVERT: C 142 ASN cc_start: 0.6999 (m-40) cc_final: 0.6764 (p0) REVERT: C 225 ASP cc_start: 0.6968 (t0) cc_final: 0.6191 (t0) REVERT: D 45 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7588 (mp) REVERT: D 142 HIS cc_start: 0.8113 (p90) cc_final: 0.7653 (p90) REVERT: G 175 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: G 187 ASN cc_start: 0.7067 (p0) cc_final: 0.6856 (p0) REVERT: G 195 TYR cc_start: 0.8160 (m-80) cc_final: 0.7841 (m-10) REVERT: G 224 ARG cc_start: 0.8023 (mtp85) cc_final: 0.6531 (mtt180) REVERT: G 245 PHE cc_start: 0.5950 (m-80) cc_final: 0.5714 (m-10) REVERT: G 314 LEU cc_start: 0.6219 (OUTLIER) cc_final: 0.5754 (mm) REVERT: H 45 LEU cc_start: 0.7649 (mm) cc_final: 0.7375 (mm) REVERT: H 100 PHE cc_start: 0.6660 (m-80) cc_final: 0.6174 (m-80) REVERT: L 89 GLN cc_start: 0.7116 (OUTLIER) cc_final: 0.6697 (tp40) outliers start: 53 outliers final: 40 residues processed: 254 average time/residue: 0.2467 time to fit residues: 95.7243 Evaluate side-chains 243 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 198 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 175 GLU Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 92 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 0 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 148 optimal weight: 0.8980 chunk 48 optimal weight: 0.0270 chunk 64 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS B 125 GLN C 282 GLN I 125 GLN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.160592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.137011 restraints weight = 22120.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.140173 restraints weight = 13915.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.142318 restraints weight = 10016.875| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14060 Z= 0.154 Angle : 0.667 19.926 19132 Z= 0.331 Chirality : 0.046 0.506 2095 Planarity : 0.004 0.052 2451 Dihedral : 5.470 55.752 2253 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.38 % Allowed : 18.86 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.02 (0.20), residues: 1684 helix: 2.01 (0.27), residues: 363 sheet: 0.06 (0.29), residues: 295 loop : -0.80 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 36 HIS 0.009 0.001 HIS A 38 PHE 0.020 0.002 PHE G 118 TYR 0.026 0.002 TYR B 119 ARG 0.010 0.001 ARG B 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00831 ( 16) link_NAG-ASN : angle 4.48878 ( 48) link_BETA1-4 : bond 0.00269 ( 4) link_BETA1-4 : angle 1.52535 ( 12) hydrogen bonds : bond 0.04533 ( 574) hydrogen bonds : angle 5.26594 ( 1650) SS BOND : bond 0.00338 ( 20) SS BOND : angle 1.18566 ( 40) covalent geometry : bond 0.00359 (14020) covalent geometry : angle 0.62621 (19032) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4407.69 seconds wall clock time: 77 minutes 40.65 seconds (4660.65 seconds total)