Starting phenix.real_space_refine on Wed Mar 4 14:11:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n7s_49098/03_2026/9n7s_49098.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n7s_49098/03_2026/9n7s_49098.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n7s_49098/03_2026/9n7s_49098.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n7s_49098/03_2026/9n7s_49098.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n7s_49098/03_2026/9n7s_49098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n7s_49098/03_2026/9n7s_49098.map" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 8685 2.51 5 N 2338 2.21 5 O 2720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13802 Number of models: 1 Model: "" Number of chains: 15 Chain: "b" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1397 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "a" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1389 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain: "L" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 863 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "c" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1397 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "C" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2504 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 18, 'TRANS': 301} Chain: "A" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2504 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 18, 'TRANS': 301} Chain: "B" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2517 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 19, 'TRANS': 302} Chain: "H" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 931 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "F" 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: "c" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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: "A" 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: "B" 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: 3.60, per 1000 atoms: 0.26 Number of scatterers: 13802 At special positions: 0 Unit cell: (89.9, 102.225, 149.35, 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 2720 8.00 N 2338 7.00 C 8685 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS b 144 " - pdb=" SG CYS b 148 " distance=2.05 Simple disulfide: pdb=" SG CYS a 144 " - pdb=" SG CYS a 148 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS c 137 " - pdb=" SG CYS C 14 " distance=2.04 Simple disulfide: pdb=" SG CYS c 144 " - pdb=" SG CYS c 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.06 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 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 " BETA1-6 " NAG D 1 " - " FUC D 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG E 1 " - " FUC E 3 " NAG-ASN " NAG A 401 " - " ASN A 21 " " NAG A 402 " - " ASN A 33 " " NAG A 403 " - " ASN A 278 " " NAG A 404 " - " ASN A 94 " " NAG A 405 " - " ASN A 289 " " NAG B 401 " - " ASN B 278 " " NAG B 402 " - " ASN B 21 " " NAG B 403 " - " ASN B 33 " " NAG B 404 " - " ASN B 289 " " NAG C 401 " - " ASN C 33 " " NAG C 402 " - " ASN C 94 " " NAG C 403 " - " ASN C 278 " " NAG C 404 " - " ASN C 21 " " NAG C 405 " - " ASN C 289 " " NAG D 1 " - " ASN b 154 " " NAG E 1 " - " ASN a 154 " " NAG F 1 " - " ASN B 94 " " NAG c 301 " - " ASN c 154 " Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 778.2 milliseconds 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3162 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 37 sheets defined 22.8% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'b' and resid 37 through 58 Processing helix chain 'b' and resid 74 through 126 removed outlier: 4.333A pdb=" N LEU b 101 " --> pdb=" O GLU b 97 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 154 Processing helix chain 'b' and resid 162 through 173 Processing helix chain 'a' and resid 37 through 58 Processing helix chain 'a' and resid 74 through 126 Processing helix chain 'a' and resid 145 through 155 Processing helix chain 'a' and resid 162 through 172 Processing helix chain 'c' and resid 37 through 58 Processing helix chain 'c' and resid 75 through 126 Processing helix chain 'c' and resid 145 through 155 Processing helix chain 'c' and resid 158 through 172 removed outlier: 3.887A pdb=" N TYR c 162 " --> pdb=" O ASP c 158 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLU c 164 " --> pdb=" O PRO c 160 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLU c 165 " --> pdb=" O LYS c 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.980A pdb=" N GLU C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'B' and resid 65 through 71 Processing helix chain 'B' and resid 73 through 77 removed outlier: 4.271A pdb=" N GLU B 77 " --> pdb=" O PRO B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 112 removed outlier: 3.881A pdb=" N LEU B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.962A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'b' and resid 33 through 34 removed outlier: 3.831A pdb=" N GLY b 23 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B 16 " --> pdb=" O GLY b 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'b' and resid 64 through 65 removed outlier: 3.924A pdb=" N THR b 64 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N CYS B 281 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE B 288 " --> pdb=" O CYS B 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 31 through 36 removed outlier: 3.751A pdb=" N GLY a 23 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS a 25 " --> pdb=" O CYS A 14 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 63 through 65 removed outlier: 3.595A pdb=" N THR a 64 " --> pdb=" O GLY A 303 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.639A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.530A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 27C through 27D removed outlier: 3.586A pdb=" N LYS L 30 " --> pdb=" O ASN L 27D" (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'c' and resid 33 through 36 removed outlier: 3.887A pdb=" N GLY c 23 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY C 16 " --> pdb=" O GLY c 23 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS C 14 " --> pdb=" O HIS c 25 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'c' and resid 64 through 65 removed outlier: 3.541A pdb=" N THR c 64 " --> pdb=" O GLY C 303 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY C 303 " --> pdb=" O THR c 64 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE C 288 " --> pdb=" O CYS C 281 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 24 through 26 removed outlier: 3.965A pdb=" N ASP C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 40 through 41 Processing sheet with id=AB3, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB4, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.037A pdb=" N LEU C 51 " --> pdb=" O HIS C 275 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR C 279 " --> pdb=" O LYS C 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 59 through 61 removed outlier: 6.311A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 115 through 122 removed outlier: 3.652A pdb=" N SER C 117 " --> pdb=" O GLU C 261 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.574A pdb=" N ALA C 138 " --> pdb=" O ALA C 144 " (cutoff:3.500A) removed outlier: 10.277A pdb=" N ALA C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 151 through 153 Processing sheet with id=AB9, first strand: chain 'C' and resid 164 through 166 Processing sheet with id=AC1, first strand: chain 'A' and resid 24 through 26 removed outlier: 4.144A pdb=" N ASP A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AC3, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AC4, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.154A pdb=" N LEU A 51 " --> pdb=" O HIS A 275 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 59 through 61 removed outlier: 6.442A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE A 87 " --> pdb=" O ILE A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'A' and resid 115 through 122 removed outlier: 3.604A pdb=" N SER A 117 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A 253 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 152 " --> pdb=" O VAL A 253 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 115 through 122 removed outlier: 3.604A pdb=" N SER A 117 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 136 through 140 Processing sheet with id=AC9, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AD1, first strand: chain 'B' and resid 24 through 26 removed outlier: 4.035A pdb=" N ASP B 24 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AD3, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AD4, first strand: chain 'B' and resid 59 through 60 removed outlier: 6.057A pdb=" N LEU B 59 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE B 87 " --> pdb=" O ILE B 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 119 through 122 removed outlier: 6.651A pdb=" N TYR B 256 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N LEU B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N LEU B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 119 through 122 removed outlier: 6.651A pdb=" N TYR B 256 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N LEU B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 164 through 166 Processing sheet with id=AD8, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.019A pdb=" N LEU H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 57 through 59 removed outlier: 4.789A pdb=" N LEU H 45 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N SER H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TRP H 34 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA H 93 " --> pdb=" O THR H 35A" (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ALA H 100H" --> pdb=" O GLN H 96 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE H 98 " --> pdb=" O GLY H 100F" (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLY H 100F" --> pdb=" O ILE H 98 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE H 100 " --> pdb=" O ILE H 100D" (cutoff:3.500A) removed outlier: 5.162A pdb=" N ILE H 100D" --> pdb=" O ILE H 100 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 57 through 59 removed outlier: 4.789A pdb=" N LEU H 45 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N SER H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TRP H 34 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA H 93 " --> pdb=" O THR H 35A" (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1476 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: 2.79 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4418 1.34 - 1.47: 3562 1.47 - 1.59: 6057 1.59 - 1.71: 0 1.71 - 1.84: 78 Bond restraints: 14115 Sorted by residual: bond pdb=" N GLY c 1 " pdb=" CA GLY c 1 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.43e+00 bond pdb=" N GLY a 1 " pdb=" CA GLY a 1 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.26e+00 bond pdb=" N GLY b 1 " pdb=" CA GLY b 1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.91e+00 bond pdb=" C CYS C 139 " pdb=" N PRO C 140 " ideal model delta sigma weight residual 1.330 1.355 -0.025 1.25e-02 6.40e+03 4.14e+00 bond pdb=" CG1 ILE B 182 " pdb=" CD1 ILE B 182 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.61e+00 ... (remaining 14110 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 18220 1.56 - 3.13: 725 3.13 - 4.69: 128 4.69 - 6.25: 53 6.25 - 7.82: 5 Bond angle restraints: 19131 Sorted by residual: angle pdb=" N GLY c 12 " pdb=" CA GLY c 12 " pdb=" C GLY c 12 " ideal model delta sigma weight residual 110.38 115.07 -4.69 1.48e+00 4.57e-01 1.00e+01 angle pdb=" C ALA C 263 " pdb=" CA ALA C 263 " pdb=" CB ALA C 263 " ideal model delta sigma weight residual 110.42 116.28 -5.86 1.99e+00 2.53e-01 8.67e+00 angle pdb=" C2 NAG B 404 " pdb=" N2 NAG B 404 " pdb=" C7 NAG B 404 " ideal model delta sigma weight residual 124.56 131.90 -7.34 3.00e+00 1.11e-01 5.99e+00 angle pdb=" CA ARG H 81 " pdb=" CB ARG H 81 " pdb=" CG ARG H 81 " ideal model delta sigma weight residual 114.10 118.86 -4.76 2.00e+00 2.50e-01 5.67e+00 angle pdb=" C2 NAG D 1 " pdb=" N2 NAG D 1 " pdb=" C7 NAG D 1 " ideal model delta sigma weight residual 124.56 131.69 -7.13 3.00e+00 1.11e-01 5.65e+00 ... (remaining 19126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 8067 17.41 - 34.81: 517 34.81 - 52.21: 86 52.21 - 69.62: 22 69.62 - 87.02: 8 Dihedral angle restraints: 8700 sinusoidal: 3750 harmonic: 4950 Sorted by residual: dihedral pdb=" CB CYS B 52 " pdb=" SG CYS B 52 " pdb=" SG CYS B 277 " pdb=" CB CYS B 277 " ideal model delta sinusoidal sigma weight residual -86.00 -5.62 -80.38 1 1.00e+01 1.00e-02 7.99e+01 dihedral pdb=" CB CYS b 144 " pdb=" SG CYS b 144 " pdb=" SG CYS b 148 " pdb=" CB CYS b 148 " ideal model delta sinusoidal sigma weight residual 93.00 25.20 67.80 1 1.00e+01 1.00e-02 5.97e+01 dihedral pdb=" CB CYS A 97 " pdb=" SG CYS A 97 " pdb=" SG CYS A 139 " pdb=" CB CYS A 139 " ideal model delta sinusoidal sigma weight residual -86.00 -152.48 66.48 1 1.00e+01 1.00e-02 5.77e+01 ... (remaining 8697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1852 0.067 - 0.134: 261 0.134 - 0.201: 25 0.201 - 0.268: 0 0.268 - 0.335: 1 Chirality restraints: 2139 Sorted by residual: chirality pdb=" C1 NAG B 404 " pdb=" ND2 ASN B 289 " pdb=" C2 NAG B 404 " pdb=" O5 NAG B 404 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" C2 NAG A 403 " pdb=" C1 NAG A 403 " pdb=" C3 NAG A 403 " pdb=" N2 NAG A 403 " both_signs ideal model delta sigma weight residual False -2.49 -2.29 -0.20 2.00e-01 2.50e+01 9.74e-01 chirality pdb=" CA THR L 94 " pdb=" N THR L 94 " pdb=" C THR L 94 " pdb=" CB THR L 94 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.32e-01 ... (remaining 2136 not shown) Planarity restraints: 2454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 98 " -0.047 5.00e-02 4.00e+02 7.13e-02 8.13e+00 pdb=" N PRO B 99 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 7 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO L 8 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 238 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO A 239 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 239 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 239 " -0.024 5.00e-02 4.00e+02 ... (remaining 2451 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 210 2.65 - 3.21: 12415 3.21 - 3.77: 21060 3.77 - 4.34: 30268 4.34 - 4.90: 51504 Nonbonded interactions: 115457 Sorted by model distance: nonbonded pdb=" OG1 THR C 283 " pdb=" O GLY C 286 " model vdw 2.082 3.040 nonbonded pdb=" OG SER b 151 " pdb=" O THR b 156 " model vdw 2.090 3.040 nonbonded pdb=" OG1 THR L 63 " pdb=" OG1 THR L 74 " model vdw 2.120 3.040 nonbonded pdb=" O CYS B 139 " pdb=" OG SER B 146 " model vdw 2.120 3.040 nonbonded pdb=" OE2 GLU b 97 " pdb=" OG SER B 311 " model vdw 2.148 3.040 ... (remaining 115452 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' and (resid 12 through 322 or resid 402 through 405)) selection = (chain 'B' and (resid 12 through 322 or resid 401 through 404)) selection = (chain 'C' and (resid 12 through 322 or resid 402 through 405)) } ncs_group { reference = (chain 'D' and resid 1) selection = (chain 'F' and resid 1) } ncs_group { reference = chain 'a' selection = (chain 'b' and resid 1 through 172) selection = (chain 'c' and resid 1 through 172) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.550 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.190 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 : 0.005 0.074 14153 Z= 0.197 Angle : 0.782 12.461 19229 Z= 0.397 Chirality : 0.049 0.335 2139 Planarity : 0.005 0.071 2436 Dihedral : 11.590 87.024 5490 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.19), residues: 1698 helix: 1.19 (0.26), residues: 375 sheet: -1.42 (0.29), residues: 291 loop : -1.60 (0.17), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG b 170 TYR 0.015 0.002 TYR A 105 PHE 0.021 0.003 PHE b 9 TRP 0.017 0.002 TRP A 153 HIS 0.006 0.001 HIS H 53 Details of bonding type rmsd covalent geometry : bond 0.00478 (14115) covalent geometry : angle 0.76472 (19131) SS BOND : bond 0.00805 ( 16) SS BOND : angle 2.35148 ( 32) hydrogen bonds : bond 0.14727 ( 509) hydrogen bonds : angle 6.89620 ( 1476) link_BETA1-4 : bond 0.02035 ( 2) link_BETA1-4 : angle 5.40792 ( 6) link_BETA1-6 : bond 0.00573 ( 2) link_BETA1-6 : angle 1.13998 ( 6) link_NAG-ASN : bond 0.00387 ( 18) link_NAG-ASN : angle 1.97215 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.477 Fit side-chains REVERT: b 39 LYS cc_start: 0.8561 (ttpt) cc_final: 0.8319 (ttpp) REVERT: b 131 LYS cc_start: 0.8289 (tttt) cc_final: 0.8063 (ttmt) REVERT: b 162 TYR cc_start: 0.7796 (m-80) cc_final: 0.7557 (m-80) REVERT: a 39 LYS cc_start: 0.8461 (tttt) cc_final: 0.8034 (ttpm) REVERT: a 143 LYS cc_start: 0.9011 (tptt) cc_final: 0.8803 (tppt) REVERT: L 36 TYR cc_start: 0.8530 (m-80) cc_final: 0.8144 (m-80) REVERT: c 2 LEU cc_start: 0.7734 (mp) cc_final: 0.7466 (mt) REVERT: c 47 LYS cc_start: 0.8445 (mttt) cc_final: 0.8237 (mttp) REVERT: c 123 ARG cc_start: 0.8323 (ttp-170) cc_final: 0.7797 (ttp80) REVERT: c 161 LYS cc_start: 0.8443 (ttpt) cc_final: 0.7944 (tttp) REVERT: C 32 LYS cc_start: 0.8391 (mttt) cc_final: 0.7911 (mptt) REVERT: C 246 GLU cc_start: 0.8150 (tt0) cc_final: 0.7891 (tt0) REVERT: A 11 ASP cc_start: 0.7259 (m-30) cc_final: 0.7041 (m-30) REVERT: A 93 ASP cc_start: 0.6772 (m-30) cc_final: 0.6496 (m-30) REVERT: A 149 LYS cc_start: 0.8404 (mmpt) cc_final: 0.8073 (mmtt) REVERT: A 310 LYS cc_start: 0.8857 (ttpt) cc_final: 0.8601 (ttpt) REVERT: B 32 LYS cc_start: 0.8638 (mttt) cc_final: 0.8124 (tptt) REVERT: B 46 LYS cc_start: 0.8363 (mmtt) cc_final: 0.7962 (mtpt) REVERT: B 246 GLU cc_start: 0.8140 (tt0) cc_final: 0.7863 (tt0) outliers start: 0 outliers final: 1 residues processed: 355 average time/residue: 0.6395 time to fit residues: 247.2009 Evaluate side-chains 207 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 43 ASN ** b 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 60 ASN c 50 ASN C 65 ASN C 111 GLN C 226 GLN C 231 ASN A 129 ASN A 322 ASN B 48 ASN B 231 ASN B 275 HIS B 282 GLN B 295 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.143373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.119041 restraints weight = 15977.014| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.26 r_work: 0.3238 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14153 Z= 0.163 Angle : 0.633 12.489 19229 Z= 0.316 Chirality : 0.048 0.541 2139 Planarity : 0.005 0.063 2436 Dihedral : 6.317 57.953 2300 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.28 % Allowed : 10.07 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.19), residues: 1698 helix: 1.68 (0.26), residues: 371 sheet: -0.92 (0.30), residues: 276 loop : -1.23 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG b 170 TYR 0.024 0.001 TYR L 49 PHE 0.017 0.002 PHE H 78 TRP 0.013 0.001 TRP A 153 HIS 0.004 0.001 HIS b 142 Details of bonding type rmsd covalent geometry : bond 0.00376 (14115) covalent geometry : angle 0.61179 (19131) SS BOND : bond 0.00359 ( 16) SS BOND : angle 1.42920 ( 32) hydrogen bonds : bond 0.04216 ( 509) hydrogen bonds : angle 5.09062 ( 1476) link_BETA1-4 : bond 0.01644 ( 2) link_BETA1-4 : angle 5.22683 ( 6) link_BETA1-6 : bond 0.00535 ( 2) link_BETA1-6 : angle 1.50416 ( 6) link_NAG-ASN : bond 0.00701 ( 18) link_NAG-ASN : angle 2.31605 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 0.462 Fit side-chains REVERT: b 39 LYS cc_start: 0.8698 (ttpt) cc_final: 0.8415 (ttpp) REVERT: b 116 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8340 (tptt) REVERT: b 121 LYS cc_start: 0.8296 (ttmm) cc_final: 0.7660 (mtmm) REVERT: b 131 LYS cc_start: 0.7994 (tttt) cc_final: 0.7788 (ttpt) REVERT: b 139 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7365 (tt0) REVERT: b 143 LYS cc_start: 0.8618 (tmtp) cc_final: 0.8214 (ttmm) REVERT: b 156 THR cc_start: 0.6856 (OUTLIER) cc_final: 0.6537 (p) REVERT: a 37 ASP cc_start: 0.7990 (t70) cc_final: 0.7168 (t70) REVERT: a 40 SER cc_start: 0.9029 (OUTLIER) cc_final: 0.8456 (p) REVERT: a 123 ARG cc_start: 0.8280 (tmm-80) cc_final: 0.7926 (ttp80) REVERT: a 143 LYS cc_start: 0.9089 (tptt) cc_final: 0.8877 (tptt) REVERT: c 57 GLU cc_start: 0.8053 (pt0) cc_final: 0.7500 (mm-30) REVERT: c 69 GLU cc_start: 0.7455 (pm20) cc_final: 0.7207 (pt0) REVERT: c 99 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8773 (tp) REVERT: c 123 ARG cc_start: 0.8200 (ttp-170) cc_final: 0.7842 (ttp80) REVERT: c 161 LYS cc_start: 0.8492 (ttpt) cc_final: 0.7913 (tttp) REVERT: c 169 ASN cc_start: 0.7904 (m-40) cc_final: 0.7485 (m-40) REVERT: C 77 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7908 (pt0) REVERT: C 246 GLU cc_start: 0.8392 (tt0) cc_final: 0.8032 (tt0) REVERT: C 261 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7389 (tp30) REVERT: C 314 LEU cc_start: 0.8836 (mt) cc_final: 0.8625 (mp) REVERT: A 55 ARG cc_start: 0.7838 (ptm160) cc_final: 0.7635 (ptt-90) REVERT: A 93 ASP cc_start: 0.6647 (m-30) cc_final: 0.6363 (m-30) REVERT: A 149 LYS cc_start: 0.8420 (mmpt) cc_final: 0.8017 (mmtt) REVERT: A 192 GLN cc_start: 0.7605 (mm-40) cc_final: 0.7209 (tp-100) REVERT: A 310 LYS cc_start: 0.8969 (ttpt) cc_final: 0.8714 (ttmm) REVERT: B 32 LYS cc_start: 0.8756 (mttt) cc_final: 0.8064 (tptt) REVERT: B 46 LYS cc_start: 0.8186 (mmtt) cc_final: 0.7901 (mtpt) REVERT: B 149 LYS cc_start: 0.8297 (ptpp) cc_final: 0.8059 (ptpt) REVERT: B 253 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.8348 (t) outliers start: 34 outliers final: 12 residues processed: 242 average time/residue: 0.6024 time to fit residues: 159.4818 Evaluate side-chains 208 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 189 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 116 LYS Chi-restraints excluded: chain b residue 156 THR Chi-restraints excluded: chain a residue 40 SER Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 39 LYS Chi-restraints excluded: chain c residue 99 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain H residue 74 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 77 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 92 optimal weight: 0.4980 chunk 154 optimal weight: 0.5980 chunk 133 optimal weight: 0.9980 chunk 58 optimal weight: 0.0970 chunk 97 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 43 ASN b 117 ASN ** b 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 ASN c 43 ASN C 18 HIS C 111 GLN A 231 ASN B 18 HIS B 48 ASN B 231 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.139439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.114379 restraints weight = 16235.626| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.32 r_work: 0.3215 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14153 Z= 0.143 Angle : 0.591 10.998 19229 Z= 0.295 Chirality : 0.046 0.434 2139 Planarity : 0.004 0.055 2436 Dihedral : 6.025 57.501 2298 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.42 % Allowed : 11.74 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.20), residues: 1698 helix: 1.91 (0.27), residues: 373 sheet: -0.77 (0.31), residues: 280 loop : -1.07 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG c 106 TYR 0.018 0.001 TYR L 49 PHE 0.015 0.002 PHE H 78 TRP 0.011 0.001 TRP A 153 HIS 0.005 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00329 (14115) covalent geometry : angle 0.57212 (19131) SS BOND : bond 0.00417 ( 16) SS BOND : angle 1.52612 ( 32) hydrogen bonds : bond 0.03851 ( 509) hydrogen bonds : angle 4.78544 ( 1476) link_BETA1-4 : bond 0.01209 ( 2) link_BETA1-4 : angle 4.72134 ( 6) link_BETA1-6 : bond 0.00351 ( 2) link_BETA1-6 : angle 1.25298 ( 6) link_NAG-ASN : bond 0.00424 ( 18) link_NAG-ASN : angle 2.05301 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 217 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 39 LYS cc_start: 0.8716 (ttpt) cc_final: 0.8510 (ttpp) REVERT: b 121 LYS cc_start: 0.8229 (ttmm) cc_final: 0.7673 (mtmm) REVERT: b 131 LYS cc_start: 0.8007 (tttt) cc_final: 0.7751 (ttpt) REVERT: b 139 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7326 (tt0) REVERT: b 143 LYS cc_start: 0.8532 (tmtp) cc_final: 0.8093 (ttmm) REVERT: b 156 THR cc_start: 0.6923 (OUTLIER) cc_final: 0.6655 (p) REVERT: a 11 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: a 39 LYS cc_start: 0.8584 (tttt) cc_final: 0.7987 (ttpm) REVERT: a 143 LYS cc_start: 0.9118 (tptt) cc_final: 0.8667 (tptt) REVERT: c 57 GLU cc_start: 0.8075 (pt0) cc_final: 0.7590 (mm-30) REVERT: c 123 ARG cc_start: 0.8137 (ttp-170) cc_final: 0.7799 (ttp80) REVERT: c 161 LYS cc_start: 0.8394 (ttpt) cc_final: 0.7786 (tttp) REVERT: c 169 ASN cc_start: 0.7762 (m110) cc_final: 0.7344 (m-40) REVERT: C 77 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7883 (pt0) REVERT: C 131 ASP cc_start: 0.8318 (t70) cc_final: 0.8085 (t70) REVERT: C 246 GLU cc_start: 0.8406 (tt0) cc_final: 0.8042 (tt0) REVERT: C 261 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7384 (tp30) REVERT: A 11 ASP cc_start: 0.7239 (m-30) cc_final: 0.6717 (m-30) REVERT: A 55 ARG cc_start: 0.7841 (ptm160) cc_final: 0.7619 (ptt-90) REVERT: A 149 LYS cc_start: 0.8385 (mmpt) cc_final: 0.7918 (mmtt) REVERT: A 192 GLN cc_start: 0.7595 (mm-40) cc_final: 0.7246 (tp40) REVERT: A 242 LYS cc_start: 0.8734 (tttm) cc_final: 0.8177 (ttmt) REVERT: A 262 ARG cc_start: 0.8762 (mtm180) cc_final: 0.8446 (mtm180) REVERT: A 310 LYS cc_start: 0.8946 (ttpt) cc_final: 0.8584 (ttmt) REVERT: B 32 LYS cc_start: 0.8753 (mttt) cc_final: 0.8046 (tptt) REVERT: B 46 LYS cc_start: 0.8200 (mmtt) cc_final: 0.7903 (mtpt) REVERT: B 149 LYS cc_start: 0.8333 (ptpp) cc_final: 0.8078 (ptpt) REVERT: B 253 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8398 (t) outliers start: 36 outliers final: 19 residues processed: 239 average time/residue: 0.5793 time to fit residues: 152.3403 Evaluate side-chains 213 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 135 ASN Chi-restraints excluded: chain b residue 156 THR Chi-restraints excluded: chain a residue 11 GLU Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 38 LEU Chi-restraints excluded: chain c residue 139 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain H residue 74 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 151 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 133 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 157 optimal weight: 0.0970 chunk 159 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 43 ASN b 128 ASN ** b 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 43 ASN C 111 GLN B 48 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.138784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113816 restraints weight = 16194.351| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.32 r_work: 0.3193 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14153 Z= 0.147 Angle : 0.580 11.114 19229 Z= 0.290 Chirality : 0.045 0.369 2139 Planarity : 0.004 0.051 2436 Dihedral : 5.970 57.872 2298 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.82 % Allowed : 12.82 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.20), residues: 1698 helix: 1.85 (0.27), residues: 385 sheet: -0.66 (0.30), residues: 290 loop : -1.01 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 123 TYR 0.017 0.001 TYR L 49 PHE 0.015 0.002 PHE H 78 TRP 0.012 0.001 TRP A 153 HIS 0.005 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00341 (14115) covalent geometry : angle 0.56339 (19131) SS BOND : bond 0.00413 ( 16) SS BOND : angle 1.42838 ( 32) hydrogen bonds : bond 0.03744 ( 509) hydrogen bonds : angle 4.67824 ( 1476) link_BETA1-4 : bond 0.01202 ( 2) link_BETA1-4 : angle 4.55638 ( 6) link_BETA1-6 : bond 0.00365 ( 2) link_BETA1-6 : angle 1.22158 ( 6) link_NAG-ASN : bond 0.00444 ( 18) link_NAG-ASN : angle 1.91825 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 205 time to evaluate : 0.564 Fit side-chains REVERT: b 39 LYS cc_start: 0.8711 (ttpt) cc_final: 0.8435 (ttpp) REVERT: b 121 LYS cc_start: 0.8158 (ttmm) cc_final: 0.7611 (mtmm) REVERT: b 131 LYS cc_start: 0.7933 (tttt) cc_final: 0.7640 (ttpt) REVERT: b 139 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7179 (tt0) REVERT: b 156 THR cc_start: 0.7027 (OUTLIER) cc_final: 0.6677 (p) REVERT: a 39 LYS cc_start: 0.8564 (tttt) cc_final: 0.7953 (ttpm) REVERT: a 143 LYS cc_start: 0.9062 (tptt) cc_final: 0.8589 (tptt) REVERT: c 57 GLU cc_start: 0.8063 (pt0) cc_final: 0.7521 (mm-30) REVERT: c 123 ARG cc_start: 0.8167 (ttp-170) cc_final: 0.7781 (ttp80) REVERT: c 161 LYS cc_start: 0.8312 (ttpt) cc_final: 0.7712 (tttp) REVERT: c 169 ASN cc_start: 0.7751 (m110) cc_final: 0.7358 (m-40) REVERT: C 77 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7837 (pt0) REVERT: C 103 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8629 (mp) REVERT: C 131 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8080 (t70) REVERT: C 246 GLU cc_start: 0.8380 (tt0) cc_final: 0.7985 (tt0) REVERT: C 260 MET cc_start: 0.8477 (ptt) cc_final: 0.8223 (ptm) REVERT: C 261 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7401 (tp30) REVERT: A 11 ASP cc_start: 0.7272 (m-30) cc_final: 0.6709 (m-30) REVERT: A 55 ARG cc_start: 0.7844 (ptm160) cc_final: 0.7637 (ptt-90) REVERT: A 149 LYS cc_start: 0.8335 (mmpt) cc_final: 0.7833 (mmtt) REVERT: A 192 GLN cc_start: 0.7483 (mm-40) cc_final: 0.7093 (tp40) REVERT: A 241 ASP cc_start: 0.8100 (m-30) cc_final: 0.7858 (m-30) REVERT: A 242 LYS cc_start: 0.8659 (tttm) cc_final: 0.8100 (ttmt) REVERT: A 262 ARG cc_start: 0.8653 (mtm180) cc_final: 0.8381 (mtm180) REVERT: A 271 ASP cc_start: 0.8548 (p0) cc_final: 0.7762 (t0) REVERT: A 310 LYS cc_start: 0.8945 (ttpt) cc_final: 0.8547 (ttmt) REVERT: B 14 CYS cc_start: 0.8560 (m) cc_final: 0.7522 (t) REVERT: B 32 LYS cc_start: 0.8727 (mttt) cc_final: 0.7968 (mptt) REVERT: B 46 LYS cc_start: 0.8117 (mmtt) cc_final: 0.7802 (mtpt) REVERT: B 149 LYS cc_start: 0.8298 (ptpp) cc_final: 0.8046 (ptpt) REVERT: B 191 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7024 (tt0) outliers start: 42 outliers final: 22 residues processed: 233 average time/residue: 0.5819 time to fit residues: 149.2710 Evaluate side-chains 221 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 32 SER Chi-restraints excluded: chain b residue 128 ASN Chi-restraints excluded: chain b residue 156 THR Chi-restraints excluded: chain a residue 15 THR Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 39 LYS Chi-restraints excluded: chain c residue 99 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 153 TRP Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain H residue 74 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 1 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 166 optimal weight: 7.9990 chunk 5 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 92 optimal weight: 0.3980 chunk 53 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 43 ASN b 128 ASN ** b 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 43 ASN C 111 GLN H 32 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.139005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.114069 restraints weight = 16211.909| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.33 r_work: 0.3189 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14153 Z= 0.145 Angle : 0.581 11.568 19229 Z= 0.291 Chirality : 0.045 0.356 2139 Planarity : 0.004 0.045 2436 Dihedral : 5.911 57.854 2298 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.95 % Allowed : 13.62 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.20), residues: 1698 helix: 2.16 (0.27), residues: 373 sheet: -0.61 (0.30), residues: 292 loop : -0.96 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG c 106 TYR 0.019 0.001 TYR L 49 PHE 0.014 0.001 PHE H 78 TRP 0.054 0.001 TRP A 153 HIS 0.004 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00335 (14115) covalent geometry : angle 0.56567 (19131) SS BOND : bond 0.00316 ( 16) SS BOND : angle 1.31778 ( 32) hydrogen bonds : bond 0.03687 ( 509) hydrogen bonds : angle 4.61956 ( 1476) link_BETA1-4 : bond 0.01267 ( 2) link_BETA1-4 : angle 4.45574 ( 6) link_BETA1-6 : bond 0.00422 ( 2) link_BETA1-6 : angle 1.41094 ( 6) link_NAG-ASN : bond 0.00408 ( 18) link_NAG-ASN : angle 1.87835 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 202 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: b 39 LYS cc_start: 0.8725 (ttpt) cc_final: 0.8450 (ttpp) REVERT: b 121 LYS cc_start: 0.8137 (ttmm) cc_final: 0.7575 (mtmm) REVERT: b 131 LYS cc_start: 0.7925 (tttt) cc_final: 0.7611 (ttpt) REVERT: b 139 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7387 (mm-30) REVERT: b 156 THR cc_start: 0.7020 (OUTLIER) cc_final: 0.6754 (p) REVERT: a 39 LYS cc_start: 0.8553 (tttt) cc_final: 0.7938 (ttpm) REVERT: a 143 LYS cc_start: 0.9065 (tptt) cc_final: 0.8596 (tptt) REVERT: c 22 TYR cc_start: 0.9272 (OUTLIER) cc_final: 0.8812 (m-80) REVERT: c 57 GLU cc_start: 0.8052 (pt0) cc_final: 0.7527 (mm-30) REVERT: c 123 ARG cc_start: 0.8143 (ttp-170) cc_final: 0.7747 (ttp80) REVERT: c 161 LYS cc_start: 0.8266 (ttpt) cc_final: 0.7712 (tttp) REVERT: c 169 ASN cc_start: 0.7722 (m110) cc_final: 0.7335 (m-40) REVERT: C 77 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7839 (pt0) REVERT: C 131 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8123 (t70) REVERT: C 246 GLU cc_start: 0.8353 (tt0) cc_final: 0.7961 (tt0) REVERT: C 260 MET cc_start: 0.8483 (ptt) cc_final: 0.8211 (ptm) REVERT: C 261 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7404 (tp30) REVERT: A 11 ASP cc_start: 0.7277 (m-30) cc_final: 0.6677 (m-30) REVERT: A 53 LYS cc_start: 0.7933 (mttt) cc_final: 0.7713 (mtmt) REVERT: A 55 ARG cc_start: 0.7823 (ptm160) cc_final: 0.7605 (ptt-90) REVERT: A 149 LYS cc_start: 0.8352 (mmpt) cc_final: 0.7854 (mmtt) REVERT: A 192 GLN cc_start: 0.7498 (mm-40) cc_final: 0.7196 (tm-30) REVERT: A 241 ASP cc_start: 0.8113 (m-30) cc_final: 0.7877 (m-30) REVERT: A 271 ASP cc_start: 0.8553 (p0) cc_final: 0.7772 (t0) REVERT: A 310 LYS cc_start: 0.8940 (ttpt) cc_final: 0.8548 (ttmt) REVERT: B 14 CYS cc_start: 0.8546 (m) cc_final: 0.7478 (t) REVERT: B 32 LYS cc_start: 0.8731 (mttt) cc_final: 0.7970 (mptt) REVERT: B 46 LYS cc_start: 0.8119 (mmtt) cc_final: 0.7796 (mtpt) REVERT: B 149 LYS cc_start: 0.8271 (ptpp) cc_final: 0.8023 (ptpt) REVERT: B 191 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7011 (tt0) REVERT: B 253 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8379 (t) REVERT: H 33 ASN cc_start: 0.8311 (m-40) cc_final: 0.7911 (t0) outliers start: 44 outliers final: 22 residues processed: 232 average time/residue: 0.5455 time to fit residues: 139.7590 Evaluate side-chains 227 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 198 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 32 SER Chi-restraints excluded: chain b residue 156 THR Chi-restraints excluded: chain a residue 15 THR Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 22 TYR Chi-restraints excluded: chain c residue 39 LYS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 312 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 134 optimal weight: 0.0870 chunk 60 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 69 optimal weight: 0.4980 chunk 93 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 43 ASN b 62 GLN ** b 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 128 ASN C 111 GLN B 48 ASN H 32 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.139095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.114097 restraints weight = 16089.702| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.31 r_work: 0.3194 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14153 Z= 0.137 Angle : 0.583 11.465 19229 Z= 0.289 Chirality : 0.045 0.343 2139 Planarity : 0.004 0.044 2436 Dihedral : 5.942 58.589 2298 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.09 % Allowed : 13.83 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.20), residues: 1698 helix: 2.00 (0.27), residues: 385 sheet: -0.56 (0.30), residues: 292 loop : -0.90 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG a 123 TYR 0.020 0.001 TYR L 49 PHE 0.013 0.001 PHE H 78 TRP 0.007 0.001 TRP H 36 HIS 0.004 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00316 (14115) covalent geometry : angle 0.56197 (19131) SS BOND : bond 0.00446 ( 16) SS BOND : angle 1.83220 ( 32) hydrogen bonds : bond 0.03640 ( 509) hydrogen bonds : angle 4.60060 ( 1476) link_BETA1-4 : bond 0.01285 ( 2) link_BETA1-4 : angle 4.36980 ( 6) link_BETA1-6 : bond 0.00978 ( 2) link_BETA1-6 : angle 2.20228 ( 6) link_NAG-ASN : bond 0.00453 ( 18) link_NAG-ASN : angle 2.12667 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 208 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: b 39 LYS cc_start: 0.8725 (ttpt) cc_final: 0.8439 (ttpp) REVERT: b 121 LYS cc_start: 0.8114 (ttmm) cc_final: 0.7539 (mtmm) REVERT: b 131 LYS cc_start: 0.7926 (tttt) cc_final: 0.7613 (ttpt) REVERT: b 139 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7376 (mm-30) REVERT: b 150 GLU cc_start: 0.7516 (pp20) cc_final: 0.7271 (pp20) REVERT: b 167 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.6756 (tptt) REVERT: a 39 LYS cc_start: 0.8565 (tttt) cc_final: 0.7960 (ttpm) REVERT: a 75 LYS cc_start: 0.8195 (tptt) cc_final: 0.7543 (tptm) REVERT: a 143 LYS cc_start: 0.9044 (tptt) cc_final: 0.8588 (tptt) REVERT: c 22 TYR cc_start: 0.9264 (OUTLIER) cc_final: 0.8813 (m-80) REVERT: c 57 GLU cc_start: 0.8046 (pt0) cc_final: 0.7553 (mm-30) REVERT: c 69 GLU cc_start: 0.7551 (pt0) cc_final: 0.7297 (pt0) REVERT: c 123 ARG cc_start: 0.8110 (ttp-170) cc_final: 0.7752 (ttp80) REVERT: c 161 LYS cc_start: 0.8230 (ttpt) cc_final: 0.7679 (tttp) REVERT: c 169 ASN cc_start: 0.7707 (m110) cc_final: 0.7411 (m-40) REVERT: C 77 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7814 (pt0) REVERT: C 131 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8124 (t70) REVERT: C 211 LYS cc_start: 0.8636 (tttt) cc_final: 0.8401 (tttm) REVERT: C 246 GLU cc_start: 0.8335 (tt0) cc_final: 0.7935 (tt0) REVERT: C 260 MET cc_start: 0.8485 (ptt) cc_final: 0.8195 (ptm) REVERT: C 261 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7431 (tp30) REVERT: C 291 SER cc_start: 0.8116 (OUTLIER) cc_final: 0.7754 (t) REVERT: A 11 ASP cc_start: 0.7282 (m-30) cc_final: 0.6668 (m-30) REVERT: A 14 CYS cc_start: 0.8976 (m) cc_final: 0.8587 (m) REVERT: A 53 LYS cc_start: 0.7938 (mttt) cc_final: 0.7729 (mtmt) REVERT: A 55 ARG cc_start: 0.7807 (ptm160) cc_final: 0.7588 (ptt-90) REVERT: A 149 LYS cc_start: 0.8388 (mmpt) cc_final: 0.7885 (mmtm) REVERT: A 192 GLN cc_start: 0.7512 (mm-40) cc_final: 0.7213 (tm-30) REVERT: A 241 ASP cc_start: 0.8090 (m-30) cc_final: 0.7711 (t0) REVERT: A 271 ASP cc_start: 0.8538 (p0) cc_final: 0.7781 (t0) REVERT: A 310 LYS cc_start: 0.8904 (ttpt) cc_final: 0.8519 (ttmt) REVERT: B 14 CYS cc_start: 0.8522 (m) cc_final: 0.7454 (t) REVERT: B 31 GLU cc_start: 0.8326 (tt0) cc_final: 0.8121 (tt0) REVERT: B 32 LYS cc_start: 0.8718 (mttt) cc_final: 0.7956 (tptt) REVERT: B 46 LYS cc_start: 0.8112 (mmtt) cc_final: 0.7785 (mtpt) REVERT: B 149 LYS cc_start: 0.8250 (ptpp) cc_final: 0.7999 (ptpt) REVERT: B 191 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7017 (tt0) REVERT: B 195 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.7649 (m-80) outliers start: 46 outliers final: 24 residues processed: 237 average time/residue: 0.5260 time to fit residues: 137.6745 Evaluate side-chains 227 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 32 SER Chi-restraints excluded: chain b residue 167 LYS Chi-restraints excluded: chain a residue 15 THR Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 22 TYR Chi-restraints excluded: chain c residue 38 LEU Chi-restraints excluded: chain c residue 39 LYS Chi-restraints excluded: chain c residue 99 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain H residue 74 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 76 optimal weight: 1.9990 chunk 156 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 81 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 106 optimal weight: 0.0060 chunk 12 optimal weight: 0.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 43 ASN ** b 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 ASN c 128 ASN C 111 GLN B 48 ASN H 32 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.140468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.115418 restraints weight = 16083.901| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.31 r_work: 0.3208 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14153 Z= 0.118 Angle : 0.559 11.660 19229 Z= 0.279 Chirality : 0.044 0.332 2139 Planarity : 0.004 0.042 2436 Dihedral : 5.780 57.408 2298 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.62 % Allowed : 14.09 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.20), residues: 1698 helix: 2.28 (0.27), residues: 373 sheet: -0.45 (0.30), residues: 292 loop : -0.87 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG a 123 TYR 0.021 0.001 TYR L 49 PHE 0.012 0.001 PHE H 78 TRP 0.007 0.001 TRP c 92 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00269 (14115) covalent geometry : angle 0.54215 (19131) SS BOND : bond 0.00296 ( 16) SS BOND : angle 1.46622 ( 32) hydrogen bonds : bond 0.03490 ( 509) hydrogen bonds : angle 4.50161 ( 1476) link_BETA1-4 : bond 0.01307 ( 2) link_BETA1-4 : angle 4.20300 ( 6) link_BETA1-6 : bond 0.00469 ( 2) link_BETA1-6 : angle 1.33090 ( 6) link_NAG-ASN : bond 0.00439 ( 18) link_NAG-ASN : angle 1.90069 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: b 39 LYS cc_start: 0.8724 (ttpt) cc_final: 0.8439 (ttpp) REVERT: b 121 LYS cc_start: 0.8107 (ttmm) cc_final: 0.7540 (mtmm) REVERT: b 131 LYS cc_start: 0.7883 (tttt) cc_final: 0.7422 (ttmt) REVERT: b 139 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7095 (mm-30) REVERT: a 39 LYS cc_start: 0.8566 (tttt) cc_final: 0.7980 (ttpm) REVERT: a 57 GLU cc_start: 0.8627 (pt0) cc_final: 0.8410 (pt0) REVERT: a 75 LYS cc_start: 0.8203 (tptt) cc_final: 0.7545 (tptm) REVERT: a 123 ARG cc_start: 0.8171 (tmm-80) cc_final: 0.7917 (ttp80) REVERT: a 143 LYS cc_start: 0.9037 (tptt) cc_final: 0.8608 (tptt) REVERT: c 57 GLU cc_start: 0.8034 (pt0) cc_final: 0.7541 (mm-30) REVERT: c 69 GLU cc_start: 0.7563 (pt0) cc_final: 0.7311 (pt0) REVERT: c 123 ARG cc_start: 0.8037 (ttp-170) cc_final: 0.7687 (ttp80) REVERT: c 161 LYS cc_start: 0.8198 (ttpt) cc_final: 0.7674 (tttp) REVERT: c 169 ASN cc_start: 0.7701 (m110) cc_final: 0.7407 (m-40) REVERT: C 77 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7806 (pt0) REVERT: C 197 ASN cc_start: 0.8609 (m-40) cc_final: 0.8393 (m110) REVERT: C 246 GLU cc_start: 0.8338 (tt0) cc_final: 0.7394 (mt-10) REVERT: C 260 MET cc_start: 0.8504 (ptt) cc_final: 0.8222 (ptm) REVERT: C 261 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7405 (tp30) REVERT: A 11 ASP cc_start: 0.7400 (m-30) cc_final: 0.6799 (m-30) REVERT: A 14 CYS cc_start: 0.8977 (m) cc_final: 0.8543 (m) REVERT: A 53 LYS cc_start: 0.7925 (mttt) cc_final: 0.7696 (mtmt) REVERT: A 149 LYS cc_start: 0.8344 (mmpt) cc_final: 0.7809 (mmtm) REVERT: A 192 GLN cc_start: 0.7494 (mm-40) cc_final: 0.7211 (tm-30) REVERT: A 241 ASP cc_start: 0.8108 (m-30) cc_final: 0.7875 (m-30) REVERT: A 262 ARG cc_start: 0.8556 (mtm180) cc_final: 0.8345 (mtm180) REVERT: A 271 ASP cc_start: 0.8530 (p0) cc_final: 0.7832 (t0) REVERT: A 310 LYS cc_start: 0.8889 (ttpt) cc_final: 0.8510 (ttmt) REVERT: B 14 CYS cc_start: 0.8443 (m) cc_final: 0.7394 (t) REVERT: B 32 LYS cc_start: 0.8715 (mttt) cc_final: 0.7946 (tptt) REVERT: B 46 LYS cc_start: 0.8108 (mmtt) cc_final: 0.7784 (mtpt) REVERT: B 149 LYS cc_start: 0.8183 (ptpp) cc_final: 0.7959 (ptpt) REVERT: B 195 TYR cc_start: 0.8229 (OUTLIER) cc_final: 0.7721 (m-80) REVERT: H 33 ASN cc_start: 0.8298 (m-40) cc_final: 0.7876 (t0) outliers start: 39 outliers final: 17 residues processed: 235 average time/residue: 0.5164 time to fit residues: 133.9318 Evaluate side-chains 213 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 32 SER Chi-restraints excluded: chain a residue 15 THR Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 39 LYS Chi-restraints excluded: chain c residue 99 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain H residue 74 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 129 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 99 optimal weight: 0.2980 chunk 100 optimal weight: 0.5980 chunk 169 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 148 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 43 ASN ** b 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 114 ASN c 128 ASN C 111 GLN A 183 HIS H 32 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.139272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.114231 restraints weight = 16043.790| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.30 r_work: 0.3191 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14153 Z= 0.141 Angle : 0.576 12.093 19229 Z= 0.287 Chirality : 0.045 0.326 2139 Planarity : 0.004 0.041 2436 Dihedral : 5.829 57.819 2298 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.68 % Allowed : 14.56 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.20), residues: 1698 helix: 2.14 (0.27), residues: 377 sheet: -0.44 (0.31), residues: 282 loop : -0.82 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG a 123 TYR 0.022 0.001 TYR L 49 PHE 0.013 0.001 PHE H 78 TRP 0.009 0.001 TRP H 36 HIS 0.004 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00330 (14115) covalent geometry : angle 0.56006 (19131) SS BOND : bond 0.00307 ( 16) SS BOND : angle 1.50071 ( 32) hydrogen bonds : bond 0.03550 ( 509) hydrogen bonds : angle 4.53606 ( 1476) link_BETA1-4 : bond 0.01261 ( 2) link_BETA1-4 : angle 4.19345 ( 6) link_BETA1-6 : bond 0.00607 ( 2) link_BETA1-6 : angle 1.25735 ( 6) link_NAG-ASN : bond 0.00459 ( 18) link_NAG-ASN : angle 1.85258 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: b 39 LYS cc_start: 0.8722 (ttpt) cc_final: 0.8439 (ttpp) REVERT: b 121 LYS cc_start: 0.8117 (ttmm) cc_final: 0.7533 (mtmm) REVERT: b 131 LYS cc_start: 0.7920 (tttt) cc_final: 0.7463 (ttmt) REVERT: b 139 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7377 (mm-30) REVERT: a 39 LYS cc_start: 0.8525 (tttt) cc_final: 0.7933 (ttpm) REVERT: a 75 LYS cc_start: 0.8184 (tptt) cc_final: 0.7519 (tptm) REVERT: a 143 LYS cc_start: 0.9008 (tptt) cc_final: 0.8569 (tptt) REVERT: c 22 TYR cc_start: 0.9250 (OUTLIER) cc_final: 0.8774 (m-80) REVERT: c 57 GLU cc_start: 0.8030 (pt0) cc_final: 0.7539 (mm-30) REVERT: c 69 GLU cc_start: 0.7650 (pt0) cc_final: 0.7377 (pt0) REVERT: c 123 ARG cc_start: 0.8079 (ttp-170) cc_final: 0.7722 (ttp80) REVERT: c 161 LYS cc_start: 0.8196 (ttpt) cc_final: 0.7680 (tttp) REVERT: c 169 ASN cc_start: 0.7579 (m110) cc_final: 0.7282 (m-40) REVERT: C 77 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7812 (pt0) REVERT: C 197 ASN cc_start: 0.8590 (m-40) cc_final: 0.8377 (m110) REVERT: C 199 ASP cc_start: 0.7959 (t0) cc_final: 0.7582 (p0) REVERT: C 246 GLU cc_start: 0.8325 (tt0) cc_final: 0.7396 (mt-10) REVERT: C 260 MET cc_start: 0.8512 (ptt) cc_final: 0.8227 (ptm) REVERT: A 11 ASP cc_start: 0.7426 (m-30) cc_final: 0.6812 (m-30) REVERT: A 14 CYS cc_start: 0.8999 (m) cc_final: 0.8563 (m) REVERT: A 53 LYS cc_start: 0.7931 (mttt) cc_final: 0.7691 (mtmt) REVERT: A 149 LYS cc_start: 0.8338 (mmpt) cc_final: 0.7808 (mmtt) REVERT: A 192 GLN cc_start: 0.7526 (mm-40) cc_final: 0.7230 (tm-30) REVERT: A 241 ASP cc_start: 0.8122 (m-30) cc_final: 0.7761 (t0) REVERT: A 271 ASP cc_start: 0.8529 (p0) cc_final: 0.7857 (t0) REVERT: A 310 LYS cc_start: 0.8893 (ttpt) cc_final: 0.8516 (ttmt) REVERT: B 14 CYS cc_start: 0.8505 (m) cc_final: 0.7423 (t) REVERT: B 32 LYS cc_start: 0.8707 (mttt) cc_final: 0.7934 (tptt) REVERT: B 46 LYS cc_start: 0.8111 (mmtt) cc_final: 0.7781 (mtpt) REVERT: B 191 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.6884 (tt0) REVERT: B 195 TYR cc_start: 0.8318 (OUTLIER) cc_final: 0.7716 (m-80) REVERT: B 225 ASP cc_start: 0.7363 (t0) cc_final: 0.7149 (t0) REVERT: H 33 ASN cc_start: 0.8350 (m-40) cc_final: 0.7908 (t0) outliers start: 40 outliers final: 23 residues processed: 231 average time/residue: 0.5420 time to fit residues: 138.2544 Evaluate side-chains 225 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 32 SER Chi-restraints excluded: chain a residue 15 THR Chi-restraints excluded: chain a residue 59 MET Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain c residue 2 LEU Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 22 TYR Chi-restraints excluded: chain c residue 39 LYS Chi-restraints excluded: chain c residue 99 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain H residue 74 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 120 optimal weight: 0.3980 chunk 60 optimal weight: 0.5980 chunk 121 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 43 ASN ** b 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 128 ASN C 111 GLN B 48 ASN H 32 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.137531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.112303 restraints weight = 16189.937| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.31 r_work: 0.3177 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14153 Z= 0.151 Angle : 0.584 12.170 19229 Z= 0.292 Chirality : 0.045 0.319 2139 Planarity : 0.004 0.041 2436 Dihedral : 5.880 58.021 2298 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.28 % Allowed : 15.10 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.20), residues: 1698 helix: 2.12 (0.27), residues: 377 sheet: -0.46 (0.31), residues: 282 loop : -0.79 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG a 123 TYR 0.023 0.001 TYR L 49 PHE 0.014 0.002 PHE H 78 TRP 0.007 0.001 TRP H 103 HIS 0.004 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00354 (14115) covalent geometry : angle 0.56872 (19131) SS BOND : bond 0.00329 ( 16) SS BOND : angle 1.47661 ( 32) hydrogen bonds : bond 0.03597 ( 509) hydrogen bonds : angle 4.55526 ( 1476) link_BETA1-4 : bond 0.01197 ( 2) link_BETA1-4 : angle 4.18053 ( 6) link_BETA1-6 : bond 0.00537 ( 2) link_BETA1-6 : angle 1.27617 ( 6) link_NAG-ASN : bond 0.00457 ( 18) link_NAG-ASN : angle 1.83963 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: b 18 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8702 (m) REVERT: b 39 LYS cc_start: 0.8723 (ttpt) cc_final: 0.8442 (ttpp) REVERT: b 121 LYS cc_start: 0.8136 (ttmm) cc_final: 0.7552 (mtmm) REVERT: b 131 LYS cc_start: 0.7960 (tttt) cc_final: 0.7491 (ttmt) REVERT: b 139 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7389 (mm-30) REVERT: b 150 GLU cc_start: 0.7589 (pp20) cc_final: 0.6741 (mp0) REVERT: a 11 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: a 39 LYS cc_start: 0.8616 (tttt) cc_final: 0.8035 (ttpm) REVERT: a 75 LYS cc_start: 0.8213 (tptt) cc_final: 0.7690 (tptm) REVERT: a 123 ARG cc_start: 0.8306 (tmm-80) cc_final: 0.8040 (ttp80) REVERT: a 143 LYS cc_start: 0.8994 (tptt) cc_final: 0.8556 (tptt) REVERT: a 158 ASP cc_start: 0.8367 (t0) cc_final: 0.8132 (t0) REVERT: c 57 GLU cc_start: 0.8027 (pt0) cc_final: 0.7561 (mm-30) REVERT: c 62 GLN cc_start: 0.8463 (mt0) cc_final: 0.7560 (pm20) REVERT: c 123 ARG cc_start: 0.8071 (ttp-170) cc_final: 0.7714 (ttp80) REVERT: c 161 LYS cc_start: 0.8188 (ttpt) cc_final: 0.7702 (tttp) REVERT: c 169 ASN cc_start: 0.7571 (m110) cc_final: 0.7283 (m-40) REVERT: C 77 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7780 (pt0) REVERT: C 131 ASP cc_start: 0.8228 (t70) cc_final: 0.7610 (t0) REVERT: C 199 ASP cc_start: 0.7991 (t0) cc_final: 0.7588 (p0) REVERT: C 246 GLU cc_start: 0.8328 (tt0) cc_final: 0.7433 (mt-10) REVERT: C 260 MET cc_start: 0.8543 (ptt) cc_final: 0.8288 (ptm) REVERT: C 261 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7459 (tp30) REVERT: A 11 ASP cc_start: 0.7448 (m-30) cc_final: 0.6827 (m-30) REVERT: A 14 CYS cc_start: 0.8993 (m) cc_final: 0.8555 (m) REVERT: A 53 LYS cc_start: 0.7996 (mttt) cc_final: 0.7719 (mtmt) REVERT: A 149 LYS cc_start: 0.8390 (mmpt) cc_final: 0.7833 (mmtt) REVERT: A 192 GLN cc_start: 0.7530 (mm-40) cc_final: 0.7232 (tm-30) REVERT: A 241 ASP cc_start: 0.8166 (m-30) cc_final: 0.7924 (m-30) REVERT: A 271 ASP cc_start: 0.8494 (p0) cc_final: 0.7896 (t0) REVERT: A 310 LYS cc_start: 0.8900 (ttpt) cc_final: 0.8492 (ttmt) REVERT: B 32 LYS cc_start: 0.8702 (mttt) cc_final: 0.7931 (tptt) REVERT: B 46 LYS cc_start: 0.8113 (mmtt) cc_final: 0.7791 (mtpt) REVERT: B 101 ASP cc_start: 0.8174 (p0) cc_final: 0.7914 (p0) REVERT: B 191 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.6963 (tt0) REVERT: B 195 TYR cc_start: 0.8364 (OUTLIER) cc_final: 0.7810 (m-80) REVERT: B 225 ASP cc_start: 0.7401 (t0) cc_final: 0.7194 (t0) REVERT: H 33 ASN cc_start: 0.8367 (m-40) cc_final: 0.7902 (t0) REVERT: H 69 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7837 (mtm) REVERT: H 100 MET cc_start: 0.8832 (mtm) cc_final: 0.8017 (mpt) outliers start: 34 outliers final: 21 residues processed: 221 average time/residue: 0.5722 time to fit residues: 139.0096 Evaluate side-chains 225 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 32 SER Chi-restraints excluded: chain a residue 11 GLU Chi-restraints excluded: chain a residue 15 THR Chi-restraints excluded: chain a residue 59 MET Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 39 LYS Chi-restraints excluded: chain c residue 99 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 16 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 68 optimal weight: 0.9990 chunk 140 optimal weight: 0.5980 chunk 133 optimal weight: 0.4980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 43 ASN ** b 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 128 ASN C 111 GLN B 192 GLN B 196 GLN B 231 ASN H 32 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.138812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113487 restraints weight = 15926.954| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.28 r_work: 0.3184 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14153 Z= 0.141 Angle : 0.577 12.340 19229 Z= 0.289 Chirality : 0.045 0.316 2139 Planarity : 0.004 0.039 2436 Dihedral : 5.857 57.898 2298 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.15 % Allowed : 15.70 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.20), residues: 1698 helix: 2.14 (0.27), residues: 377 sheet: -0.43 (0.31), residues: 282 loop : -0.78 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG a 123 TYR 0.024 0.001 TYR L 49 PHE 0.013 0.001 PHE H 78 TRP 0.007 0.001 TRP H 103 HIS 0.004 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00331 (14115) covalent geometry : angle 0.56269 (19131) SS BOND : bond 0.00319 ( 16) SS BOND : angle 1.41611 ( 32) hydrogen bonds : bond 0.03557 ( 509) hydrogen bonds : angle 4.52488 ( 1476) link_BETA1-4 : bond 0.01190 ( 2) link_BETA1-4 : angle 4.12137 ( 6) link_BETA1-6 : bond 0.00544 ( 2) link_BETA1-6 : angle 1.26053 ( 6) link_NAG-ASN : bond 0.00460 ( 18) link_NAG-ASN : angle 1.79473 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: b 18 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8723 (m) REVERT: b 39 LYS cc_start: 0.8746 (ttpt) cc_final: 0.8480 (ttpp) REVERT: b 121 LYS cc_start: 0.8261 (ttmm) cc_final: 0.7696 (mtmm) REVERT: b 131 LYS cc_start: 0.8044 (tttt) cc_final: 0.7381 (ttmt) REVERT: b 139 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7119 (mp0) REVERT: b 150 GLU cc_start: 0.7677 (pp20) cc_final: 0.6803 (mp0) REVERT: a 11 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: a 75 LYS cc_start: 0.8275 (tptt) cc_final: 0.7623 (tptm) REVERT: a 123 ARG cc_start: 0.8337 (tmm-80) cc_final: 0.8045 (ttp80) REVERT: a 143 LYS cc_start: 0.9005 (tptt) cc_final: 0.8597 (tptt) REVERT: a 158 ASP cc_start: 0.8420 (t0) cc_final: 0.8179 (t0) REVERT: c 57 GLU cc_start: 0.8085 (pt0) cc_final: 0.7654 (mm-30) REVERT: c 62 GLN cc_start: 0.8487 (mt0) cc_final: 0.7695 (pm20) REVERT: c 123 ARG cc_start: 0.8091 (ttp-170) cc_final: 0.7757 (ttp80) REVERT: c 161 LYS cc_start: 0.8220 (ttpt) cc_final: 0.7770 (tttp) REVERT: c 169 ASN cc_start: 0.7638 (m110) cc_final: 0.7367 (m110) REVERT: C 77 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7810 (pt0) REVERT: C 131 ASP cc_start: 0.8281 (t70) cc_final: 0.7657 (t0) REVERT: C 199 ASP cc_start: 0.7970 (t0) cc_final: 0.7608 (p0) REVERT: C 246 GLU cc_start: 0.8321 (tt0) cc_final: 0.7468 (mt-10) REVERT: C 260 MET cc_start: 0.8589 (ptt) cc_final: 0.8356 (ptm) REVERT: C 261 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7494 (tp30) REVERT: A 11 ASP cc_start: 0.7498 (m-30) cc_final: 0.6890 (m-30) REVERT: A 14 CYS cc_start: 0.8973 (m) cc_final: 0.8570 (m) REVERT: A 53 LYS cc_start: 0.8102 (mttt) cc_final: 0.7860 (mtmt) REVERT: A 149 LYS cc_start: 0.8420 (mmpt) cc_final: 0.7904 (mmtt) REVERT: A 192 GLN cc_start: 0.7572 (mm-40) cc_final: 0.7302 (tm-30) REVERT: A 241 ASP cc_start: 0.8207 (m-30) cc_final: 0.7864 (t0) REVERT: A 271 ASP cc_start: 0.8492 (p0) cc_final: 0.7963 (t0) REVERT: A 310 LYS cc_start: 0.8910 (ttpt) cc_final: 0.8536 (ttmt) REVERT: B 32 LYS cc_start: 0.8713 (mttt) cc_final: 0.7985 (tptt) REVERT: B 46 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7878 (mtpt) REVERT: B 101 ASP cc_start: 0.8139 (p0) cc_final: 0.7894 (p0) REVERT: B 191 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.6986 (tt0) REVERT: B 195 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7779 (m-80) REVERT: H 33 ASN cc_start: 0.8379 (m-40) cc_final: 0.7954 (t0) REVERT: H 100 MET cc_start: 0.8834 (mtm) cc_final: 0.8116 (mpt) outliers start: 32 outliers final: 23 residues processed: 210 average time/residue: 0.5698 time to fit residues: 131.9939 Evaluate side-chains 220 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 32 SER Chi-restraints excluded: chain b residue 149 MET Chi-restraints excluded: chain a residue 11 GLU Chi-restraints excluded: chain a residue 15 THR Chi-restraints excluded: chain a residue 59 MET Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 39 LYS Chi-restraints excluded: chain c residue 99 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain H residue 74 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 66 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 24 optimal weight: 0.3980 chunk 79 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 43 ASN ** b 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 128 ASN C 111 GLN B 48 ASN B 196 GLN H 32 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.137339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.112041 restraints weight = 16154.251| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.30 r_work: 0.3171 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14153 Z= 0.158 Angle : 0.590 12.320 19229 Z= 0.296 Chirality : 0.045 0.315 2139 Planarity : 0.004 0.039 2436 Dihedral : 5.896 58.103 2298 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.35 % Allowed : 15.64 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.20), residues: 1698 helix: 2.13 (0.27), residues: 377 sheet: -0.43 (0.31), residues: 282 loop : -0.78 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG a 123 TYR 0.025 0.001 TYR L 49 PHE 0.014 0.002 PHE H 78 TRP 0.007 0.001 TRP H 103 HIS 0.004 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00372 (14115) covalent geometry : angle 0.57583 (19131) SS BOND : bond 0.00335 ( 16) SS BOND : angle 1.45617 ( 32) hydrogen bonds : bond 0.03609 ( 509) hydrogen bonds : angle 4.55792 ( 1476) link_BETA1-4 : bond 0.01154 ( 2) link_BETA1-4 : angle 4.13649 ( 6) link_BETA1-6 : bond 0.00613 ( 2) link_BETA1-6 : angle 1.26611 ( 6) link_NAG-ASN : bond 0.00470 ( 18) link_NAG-ASN : angle 1.79806 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4793.35 seconds wall clock time: 82 minutes 43.92 seconds (4963.92 seconds total)