Starting phenix.real_space_refine on Thu Mar 5 01:00:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n7q_49097/03_2026/9n7q_49097.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n7q_49097/03_2026/9n7q_49097.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n7q_49097/03_2026/9n7q_49097.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n7q_49097/03_2026/9n7q_49097.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n7q_49097/03_2026/9n7q_49097.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n7q_49097/03_2026/9n7q_49097.map" } resolution = 3.18 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= 0.016 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 75 5.16 5 C 10911 2.51 5 N 2958 2.21 5 O 3447 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 17391 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "A" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2562 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 18, 'TRANS': 308} Chain: "a" Number of atoms: 1376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1376 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 1, 'TRANS': 168} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "a" 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 Restraints were copied for chains: E, D, G, F, B, C, b, c, J, K Time building chain proxies: 3.29, per 1000 atoms: 0.19 Number of scatterers: 17391 At special positions: 0 Unit cell: (121.8, 129.775, 155.15, 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 75 16.00 O 3447 8.00 N 2958 7.00 C 10911 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 93 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS a 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 146 " distance=2.03 Simple disulfide: pdb=" SG CYS a 144 " - pdb=" SG CYS a 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 93 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 93 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS b 137 " distance=2.04 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS c 137 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 77 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 77 " distance=2.03 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 146 " distance=2.03 Simple disulfide: pdb=" SG CYS C 100 " - pdb=" SG CYS C 146 " distance=2.03 Simple disulfide: pdb=" SG CYS b 144 " - pdb=" SG CYS b 148 " distance=2.03 Simple disulfide: pdb=" SG CYS c 144 " - pdb=" SG CYS c 148 " 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A 401 " - " ASN A 21 " " NAG A 402 " - " ASN A 33 " " NAG A 403 " - " ASN A 286 " " NAG A 404 " - " ASN A 297 " " NAG A 405 " - " ASN A 172 " " NAG B 401 " - " ASN B 21 " " NAG B 402 " - " ASN B 33 " " NAG B 403 " - " ASN B 286 " " NAG B 404 " - " ASN B 297 " " NAG B 405 " - " ASN B 172 " " NAG C 401 " - " ASN C 21 " " NAG C 402 " - " ASN C 33 " " NAG C 403 " - " ASN C 286 " " NAG C 404 " - " ASN C 297 " " NAG C 405 " - " ASN C 172 " " NAG I 1 " - " ASN A 97 " " NAG J 1 " - " ASN B 97 " " NAG K 1 " - " ASN C 97 " " NAG a 301 " - " ASN a 154 " " NAG b 301 " - " ASN b 154 " " NAG c 301 " - " ASN c 154 " Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 744.2 milliseconds 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3990 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 42 sheets defined 18.3% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.122A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 72 Processing helix chain 'A' and resid 107 through 115 removed outlier: 3.661A pdb=" N LEU A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 202 Processing helix chain 'a' and resid 37 through 58 removed outlier: 3.670A pdb=" N LYS a 58 " --> pdb=" O SER a 54 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 127 Processing helix chain 'a' and resid 145 through 155 Processing helix chain 'a' and resid 158 through 173 removed outlier: 3.847A pdb=" N TYR a 162 " --> pdb=" O ASP a 158 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU a 164 " --> pdb=" O PRO a 160 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLU a 165 " --> pdb=" O LYS a 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 4.122A pdb=" N PHE G 83 " --> pdb=" O SER G 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 72 Processing helix chain 'B' and resid 107 through 115 removed outlier: 3.660A pdb=" N LEU B 111 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 202 Processing helix chain 'b' and resid 37 through 58 removed outlier: 3.670A pdb=" N LYS b 58 " --> pdb=" O SER b 54 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 127 Processing helix chain 'b' and resid 145 through 155 Processing helix chain 'b' and resid 158 through 173 removed outlier: 3.847A pdb=" N TYR b 162 " --> pdb=" O ASP b 158 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU b 164 " --> pdb=" O PRO b 160 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLU b 165 " --> pdb=" O LYS b 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.122A pdb=" N PHE F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 72 Processing helix chain 'C' and resid 107 through 115 removed outlier: 3.661A pdb=" N LEU C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 202 Processing helix chain 'c' and resid 37 through 58 removed outlier: 3.670A pdb=" N LYS c 58 " --> pdb=" O SER c 54 " (cutoff:3.500A) Processing helix chain 'c' and resid 74 through 127 Processing helix chain 'c' and resid 145 through 155 Processing helix chain 'c' and resid 158 through 173 removed outlier: 3.847A pdb=" N TYR c 162 " --> pdb=" O ASP c 158 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU c 164 " --> pdb=" O PRO c 160 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLU c 165 " --> pdb=" O LYS c 161 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.095A pdb=" N LEU H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.897A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLY H 33 " --> pdb=" O GLY H 96 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 5 removed outlier: 4.737A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.964A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 33 through 34 removed outlier: 3.655A pdb=" N HIS a 26 " --> pdb=" O GLY a 33 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY a 23 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 16 " --> pdb=" O GLY a 23 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 24 through 26 removed outlier: 4.156A pdb=" N ASP A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA8, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA9, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.201A pdb=" N LEU A 51 " --> pdb=" O HIS A 283 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N CYS A 285 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 60 through 63 removed outlier: 6.249A pdb=" N LEU A 60 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 158 through 160 Processing sheet with id=AB3, first strand: chain 'A' and resid 171 through 176 Processing sheet with id=AB4, first strand: chain 'A' and resid 238 through 244 removed outlier: 3.832A pdb=" N GLU A 182 " --> pdb=" O MET A 267 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 289 through 290 Processing sheet with id=AB6, first strand: chain 'E' and resid 3 through 7 removed outlier: 4.095A pdb=" N LEU E 78 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.897A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ALA E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N MET E 34 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLY E 33 " --> pdb=" O GLY E 96 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 4 through 5 removed outlier: 4.737A pdb=" N THR G 69 " --> pdb=" O ALA G 25 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.964A pdb=" N LEU G 11 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA G 34 " --> pdb=" O GLN G 89 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE G 48 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR G 53 " --> pdb=" O TYR G 49 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'b' and resid 33 through 34 removed outlier: 3.656A pdb=" N HIS b 26 " --> pdb=" O GLY b 33 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY b 23 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY B 16 " --> pdb=" O GLY b 23 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 24 through 26 removed outlier: 4.156A pdb=" N ASP B 24 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AC4, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AC5, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.201A pdb=" N LEU B 51 " --> pdb=" O HIS B 283 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N CYS B 285 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 60 through 63 removed outlier: 6.249A pdb=" N LEU B 60 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 158 through 160 Processing sheet with id=AC8, first strand: chain 'B' and resid 171 through 176 Processing sheet with id=AC9, first strand: chain 'B' and resid 238 through 244 removed outlier: 3.832A pdb=" N GLU B 182 " --> pdb=" O MET B 267 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 289 through 290 Processing sheet with id=AD2, first strand: chain 'D' and resid 3 through 7 removed outlier: 4.095A pdb=" N LEU D 78 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.897A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ALA D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N MET D 34 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLY D 33 " --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 4 through 5 removed outlier: 4.738A pdb=" N THR F 69 " --> pdb=" O ALA F 25 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.963A pdb=" N LEU F 11 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA F 34 " --> pdb=" O GLN F 89 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE F 48 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLN F 37 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LEU F 46 " --> pdb=" O GLN F 37 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR F 53 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'c' and resid 33 through 34 removed outlier: 3.655A pdb=" N HIS c 26 " --> pdb=" O GLY c 33 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY c 23 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY C 16 " --> pdb=" O GLY c 23 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 24 through 26 removed outlier: 4.156A pdb=" N ASP C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AD9, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AE1, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.201A pdb=" N LEU C 51 " --> pdb=" O HIS C 283 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N CYS C 285 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 60 through 63 removed outlier: 6.249A pdb=" N LEU C 60 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 158 through 160 Processing sheet with id=AE4, first strand: chain 'C' and resid 171 through 176 Processing sheet with id=AE5, first strand: chain 'C' and resid 238 through 244 removed outlier: 3.833A pdb=" N GLU C 182 " --> pdb=" O MET C 267 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 289 through 290 570 hydrogen bonds defined for protein. 1566 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: 2.41 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4525 1.33 - 1.45: 3698 1.45 - 1.57: 9456 1.57 - 1.70: 0 1.70 - 1.82: 102 Bond restraints: 17781 Sorted by residual: bond pdb=" N ILE a 6 " pdb=" CA ILE a 6 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.46e+00 bond pdb=" N ILE b 6 " pdb=" CA ILE b 6 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.42e+00 bond pdb=" N ILE c 6 " pdb=" CA ILE c 6 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.39e+00 bond pdb=" C HIS A 306 " pdb=" N PRO A 307 " ideal model delta sigma weight residual 1.336 1.364 -0.028 1.20e-02 6.94e+03 5.45e+00 bond pdb=" C HIS B 306 " pdb=" N PRO B 307 " ideal model delta sigma weight residual 1.336 1.364 -0.028 1.20e-02 6.94e+03 5.32e+00 ... (remaining 17776 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 23190 1.97 - 3.95: 759 3.95 - 5.92: 135 5.92 - 7.89: 21 7.89 - 9.86: 3 Bond angle restraints: 24108 Sorted by residual: angle pdb=" N TRP G 94 " pdb=" CA TRP G 94 " pdb=" C TRP G 94 " ideal model delta sigma weight residual 109.81 119.67 -9.86 2.21e+00 2.05e-01 1.99e+01 angle pdb=" N TRP L 94 " pdb=" CA TRP L 94 " pdb=" C TRP L 94 " ideal model delta sigma weight residual 109.81 119.66 -9.85 2.21e+00 2.05e-01 1.99e+01 angle pdb=" N TRP F 94 " pdb=" CA TRP F 94 " pdb=" C TRP F 94 " ideal model delta sigma weight residual 109.81 119.64 -9.83 2.21e+00 2.05e-01 1.98e+01 angle pdb=" C PHE c 9 " pdb=" CA PHE c 9 " pdb=" CB PHE c 9 " ideal model delta sigma weight residual 110.78 104.79 5.99 1.60e+00 3.91e-01 1.40e+01 angle pdb=" C PHE a 9 " pdb=" CA PHE a 9 " pdb=" CB PHE a 9 " ideal model delta sigma weight residual 110.78 104.79 5.99 1.60e+00 3.91e-01 1.40e+01 ... (remaining 24103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 10067 17.95 - 35.91: 661 35.91 - 53.86: 96 53.86 - 71.81: 36 71.81 - 89.77: 18 Dihedral angle restraints: 10878 sinusoidal: 4605 harmonic: 6273 Sorted by residual: dihedral pdb=" CA PRO F 95 " pdb=" C PRO F 95 " pdb=" N PRO F 96 " pdb=" CA PRO F 96 " ideal model delta harmonic sigma weight residual 180.00 151.53 28.47 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA PRO G 95 " pdb=" C PRO G 95 " pdb=" N PRO G 96 " pdb=" CA PRO G 96 " ideal model delta harmonic sigma weight residual 180.00 151.54 28.46 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA PRO L 95 " pdb=" C PRO L 95 " pdb=" N PRO L 96 " pdb=" CA PRO L 96 " ideal model delta harmonic sigma weight residual 180.00 151.56 28.44 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 10875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2481 0.095 - 0.190: 183 0.190 - 0.285: 6 0.285 - 0.380: 3 0.380 - 0.475: 3 Chirality restraints: 2676 Sorted by residual: chirality pdb=" C1 NAG A 405 " pdb=" ND2 ASN A 172 " pdb=" C2 NAG A 405 " pdb=" O5 NAG A 405 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" C1 NAG B 405 " pdb=" ND2 ASN B 172 " pdb=" C2 NAG B 405 " pdb=" O5 NAG B 405 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" C1 NAG C 405 " pdb=" ND2 ASN C 172 " pdb=" C2 NAG C 405 " pdb=" O5 NAG C 405 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.63e+00 ... (remaining 2673 not shown) Planarity restraints: 3108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP F 94 " 0.036 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO F 95 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO F 95 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 95 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP L 94 " -0.036 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO L 95 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP G 94 " 0.036 5.00e-02 4.00e+02 5.31e-02 4.52e+00 pdb=" N PRO G 95 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO G 95 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 95 " 0.030 5.00e-02 4.00e+02 ... (remaining 3105 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 176 2.62 - 3.19: 15404 3.19 - 3.76: 26388 3.76 - 4.33: 37475 4.33 - 4.90: 65284 Nonbonded interactions: 144727 Sorted by model distance: nonbonded pdb=" OG SER B 319 " pdb=" OE2 GLU b 97 " model vdw 2.048 3.040 nonbonded pdb=" OG SER A 319 " pdb=" OE2 GLU a 97 " model vdw 2.048 3.040 nonbonded pdb=" OG SER C 319 " pdb=" OE2 GLU c 97 " model vdw 2.049 3.040 nonbonded pdb=" OG SER a 151 " pdb=" O THR a 156 " model vdw 2.094 3.040 nonbonded pdb=" OG SER c 151 " pdb=" O THR c 156 " model vdw 2.094 3.040 ... (remaining 144722 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'H' selection = chain 'E' selection = chain 'D' } ncs_group { reference = chain 'L' selection = chain 'G' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.240 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: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.520 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 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 0.061 17823 Z= 0.228 Angle : 0.851 9.863 24216 Z= 0.453 Chirality : 0.053 0.475 2676 Planarity : 0.006 0.057 3087 Dihedral : 12.933 89.768 6834 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % 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: -1.40 (0.17), residues: 2157 helix: 1.22 (0.26), residues: 360 sheet: -0.70 (0.26), residues: 414 loop : -1.69 (0.15), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG c 106 TYR 0.023 0.002 TYR A 202 PHE 0.018 0.002 PHE C 105 TRP 0.026 0.002 TRP A 160 HIS 0.008 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00500 (17781) covalent geometry : angle 0.84271 (24108) SS BOND : bond 0.00450 ( 18) SS BOND : angle 1.34591 ( 36) hydrogen bonds : bond 0.12955 ( 570) hydrogen bonds : angle 7.13608 ( 1566) link_BETA1-4 : bond 0.00220 ( 3) link_BETA1-4 : angle 1.18052 ( 9) link_NAG-ASN : bond 0.00427 ( 21) link_NAG-ASN : angle 2.25864 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 81 GLN cc_start: 0.7290 (tp40) cc_final: 0.7063 (tp40) REVERT: A 23 THR cc_start: 0.9208 (p) cc_final: 0.9006 (t) REVERT: A 71 ILE cc_start: 0.8195 (tp) cc_final: 0.7794 (tp) REVERT: A 135 ASN cc_start: 0.6590 (m-40) cc_final: 0.6065 (t0) REVERT: A 233 GLN cc_start: 0.6577 (mm-40) cc_final: 0.6299 (mm-40) REVERT: A 248 ASP cc_start: 0.7032 (m-30) cc_final: 0.6736 (m-30) REVERT: B 23 THR cc_start: 0.9250 (p) cc_final: 0.9041 (t) REVERT: B 71 ILE cc_start: 0.8214 (tp) cc_final: 0.7809 (tp) REVERT: B 135 ASN cc_start: 0.6500 (m-40) cc_final: 0.6003 (t0) REVERT: B 233 GLN cc_start: 0.6564 (mm-40) cc_final: 0.6290 (mm-40) REVERT: B 248 ASP cc_start: 0.6991 (m-30) cc_final: 0.6639 (m-30) REVERT: b 75 LYS cc_start: 0.8538 (tptt) cc_final: 0.8197 (tttt) REVERT: b 124 ASN cc_start: 0.7941 (m110) cc_final: 0.7724 (m-40) REVERT: D 81 GLN cc_start: 0.7381 (tp40) cc_final: 0.7142 (tp40) REVERT: C 23 THR cc_start: 0.9214 (p) cc_final: 0.9009 (t) REVERT: C 135 ASN cc_start: 0.6534 (m-40) cc_final: 0.5976 (t0) REVERT: C 233 GLN cc_start: 0.6487 (mm-40) cc_final: 0.6069 (mm-40) REVERT: C 248 ASP cc_start: 0.7097 (m-30) cc_final: 0.6747 (m-30) REVERT: c 75 LYS cc_start: 0.8627 (tptt) cc_final: 0.8279 (tttt) outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.1332 time to fit residues: 68.9739 Evaluate side-chains 251 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.0030 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.5980 chunk 212 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN A 18 HIS ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN A 270 ASN A 303 GLN a 95 ASN ** a 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 GLN B 18 HIS ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN B 270 ASN B 303 GLN b 95 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN C 18 HIS ** C 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN C 270 ASN C 303 GLN c 95 ASN ** c 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.161889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.137376 restraints weight = 22902.274| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.33 r_work: 0.3503 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17823 Z= 0.151 Angle : 0.604 10.061 24216 Z= 0.312 Chirality : 0.046 0.425 2676 Planarity : 0.005 0.046 3087 Dihedral : 5.739 59.364 2877 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.50 % Allowed : 7.22 % Favored : 91.28 % 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: -1.17 (0.17), residues: 2157 helix: 1.59 (0.25), residues: 357 sheet: -0.79 (0.26), residues: 441 loop : -1.50 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG b 170 TYR 0.019 0.002 TYR G 91 PHE 0.011 0.001 PHE A 105 TRP 0.016 0.002 TRP L 94 HIS 0.004 0.001 HIS a 25 Details of bonding type rmsd covalent geometry : bond 0.00359 (17781) covalent geometry : angle 0.59177 (24108) SS BOND : bond 0.00278 ( 18) SS BOND : angle 0.90400 ( 36) hydrogen bonds : bond 0.04051 ( 570) hydrogen bonds : angle 5.92603 ( 1566) link_BETA1-4 : bond 0.00269 ( 3) link_BETA1-4 : angle 0.78225 ( 9) link_NAG-ASN : bond 0.00312 ( 21) link_NAG-ASN : angle 2.36629 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 274 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.7917 (ptm-80) cc_final: 0.7550 (ptp-110) REVERT: A 23 THR cc_start: 0.9274 (p) cc_final: 0.9024 (t) REVERT: A 135 ASN cc_start: 0.6689 (m-40) cc_final: 0.6170 (t0) REVERT: A 233 GLN cc_start: 0.6647 (mm-40) cc_final: 0.6427 (mm-40) REVERT: A 248 ASP cc_start: 0.7431 (m-30) cc_final: 0.7177 (m-30) REVERT: a 112 ASP cc_start: 0.8088 (m-30) cc_final: 0.7723 (m-30) REVERT: a 149 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7708 (mtt) REVERT: G 54 ARG cc_start: 0.8526 (mtp-110) cc_final: 0.8283 (mtp-110) REVERT: G 71 PHE cc_start: 0.7278 (m-80) cc_final: 0.7067 (m-80) REVERT: B 23 THR cc_start: 0.9324 (p) cc_final: 0.9064 (t) REVERT: B 135 ASN cc_start: 0.6714 (m-40) cc_final: 0.6029 (t0) REVERT: B 233 GLN cc_start: 0.6581 (mm-40) cc_final: 0.6315 (mm-40) REVERT: B 248 ASP cc_start: 0.7451 (m-30) cc_final: 0.7173 (m-30) REVERT: F 24 ARG cc_start: 0.7965 (ptm-80) cc_final: 0.7484 (ptp-110) REVERT: C 23 THR cc_start: 0.9288 (p) cc_final: 0.9041 (t) REVERT: C 135 ASN cc_start: 0.6694 (m-40) cc_final: 0.6143 (t0) REVERT: C 233 GLN cc_start: 0.6589 (mm-40) cc_final: 0.6150 (mm-40) REVERT: C 248 ASP cc_start: 0.7515 (m-30) cc_final: 0.7199 (m-30) REVERT: c 17 MET cc_start: 0.8239 (mtt) cc_final: 0.8002 (mtt) REVERT: c 90 ASP cc_start: 0.7780 (m-30) cc_final: 0.7509 (m-30) outliers start: 28 outliers final: 16 residues processed: 292 average time/residue: 0.1276 time to fit residues: 55.7233 Evaluate side-chains 261 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 244 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 149 MET Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain c residue 61 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 25 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 148 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN A 18 HIS ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN ** a 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 GLN B 18 HIS ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS ** C 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.156611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.131899 restraints weight = 23133.365| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.34 r_work: 0.3460 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17823 Z= 0.171 Angle : 0.606 10.056 24216 Z= 0.311 Chirality : 0.046 0.371 2676 Planarity : 0.005 0.043 3087 Dihedral : 5.759 58.470 2877 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.87 % Allowed : 9.68 % Favored : 88.44 % 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: -1.12 (0.17), residues: 2157 helix: 1.65 (0.25), residues: 360 sheet: -1.04 (0.24), residues: 468 loop : -1.35 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG b 170 TYR 0.018 0.002 TYR B 155 PHE 0.013 0.002 PHE C 105 TRP 0.018 0.002 TRP A 160 HIS 0.005 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00417 (17781) covalent geometry : angle 0.59547 (24108) SS BOND : bond 0.00326 ( 18) SS BOND : angle 0.83624 ( 36) hydrogen bonds : bond 0.03882 ( 570) hydrogen bonds : angle 5.78168 ( 1566) link_BETA1-4 : bond 0.00290 ( 3) link_BETA1-4 : angle 0.86495 ( 9) link_NAG-ASN : bond 0.00352 ( 21) link_NAG-ASN : angle 2.19418 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 259 time to evaluate : 0.511 Fit side-chains REVERT: L 24 ARG cc_start: 0.7968 (ptm-80) cc_final: 0.7539 (ptp-110) REVERT: L 71 PHE cc_start: 0.7722 (m-80) cc_final: 0.7472 (m-80) REVERT: A 23 THR cc_start: 0.9273 (p) cc_final: 0.9003 (t) REVERT: A 135 ASN cc_start: 0.6769 (m-40) cc_final: 0.6231 (t0) REVERT: A 197 ASP cc_start: 0.7592 (t0) cc_final: 0.7282 (t0) REVERT: A 233 GLN cc_start: 0.6691 (mm-40) cc_final: 0.6339 (mm-40) REVERT: A 318 LYS cc_start: 0.8808 (tptt) cc_final: 0.8570 (tptp) REVERT: a 90 ASP cc_start: 0.7866 (m-30) cc_final: 0.7630 (m-30) REVERT: a 149 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7750 (mtt) REVERT: E 81 GLN cc_start: 0.7354 (tp40) cc_final: 0.6910 (tm-30) REVERT: B 25 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8432 (p) REVERT: B 135 ASN cc_start: 0.6782 (m-40) cc_final: 0.6186 (t0) REVERT: B 233 GLN cc_start: 0.6767 (mm-40) cc_final: 0.6127 (mm-40) REVERT: B 318 LYS cc_start: 0.8780 (tptt) cc_final: 0.8534 (tptp) REVERT: b 10 ILE cc_start: 0.8780 (mp) cc_final: 0.8522 (mm) REVERT: D 66 ARG cc_start: 0.6856 (mmp-170) cc_final: 0.6517 (mmp-170) REVERT: F 24 ARG cc_start: 0.8073 (ptm-80) cc_final: 0.7635 (ptp-110) REVERT: F 93 ASN cc_start: 0.7013 (t0) cc_final: 0.6664 (t0) REVERT: C 135 ASN cc_start: 0.6833 (m-40) cc_final: 0.6193 (t0) REVERT: C 233 GLN cc_start: 0.6545 (mm-40) cc_final: 0.6119 (mm-40) REVERT: C 318 LYS cc_start: 0.8850 (tptt) cc_final: 0.8595 (tptp) REVERT: c 75 LYS cc_start: 0.8615 (tptt) cc_final: 0.8084 (tttt) REVERT: c 90 ASP cc_start: 0.7810 (m-30) cc_final: 0.7591 (m-30) outliers start: 35 outliers final: 23 residues processed: 278 average time/residue: 0.1332 time to fit residues: 55.2816 Evaluate side-chains 256 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 231 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 149 MET Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain c residue 61 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 107 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 71 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 151 optimal weight: 0.2980 chunk 41 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 HIS A 198 GLN a 124 ASN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS B 139 ASN B 198 GLN B 203 GLN ** b 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 GLN c 124 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.157966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.133242 restraints weight = 23050.103| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.35 r_work: 0.3480 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17823 Z= 0.136 Angle : 0.570 9.864 24216 Z= 0.290 Chirality : 0.045 0.355 2676 Planarity : 0.004 0.042 3087 Dihedral : 5.674 56.889 2877 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.61 % Allowed : 11.77 % Favored : 86.62 % 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: -0.98 (0.18), residues: 2157 helix: 1.88 (0.26), residues: 360 sheet: -1.07 (0.24), residues: 474 loop : -1.25 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 84 TYR 0.014 0.001 TYR D 100 PHE 0.010 0.001 PHE C 105 TRP 0.019 0.002 TRP F 94 HIS 0.002 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00322 (17781) covalent geometry : angle 0.55983 (24108) SS BOND : bond 0.00251 ( 18) SS BOND : angle 0.62989 ( 36) hydrogen bonds : bond 0.03684 ( 570) hydrogen bonds : angle 5.62213 ( 1566) link_BETA1-4 : bond 0.00299 ( 3) link_BETA1-4 : angle 0.87871 ( 9) link_NAG-ASN : bond 0.00329 ( 21) link_NAG-ASN : angle 2.11495 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 254 time to evaluate : 0.630 Fit side-chains REVERT: L 24 ARG cc_start: 0.7957 (ptm-80) cc_final: 0.7571 (ptp-110) REVERT: L 71 PHE cc_start: 0.7774 (m-80) cc_final: 0.7504 (m-80) REVERT: A 23 THR cc_start: 0.9250 (p) cc_final: 0.8986 (t) REVERT: A 135 ASN cc_start: 0.6698 (m-40) cc_final: 0.6210 (t0) REVERT: a 149 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7679 (mtt) REVERT: E 66 ARG cc_start: 0.6961 (mmp-170) cc_final: 0.6594 (mmp-170) REVERT: E 81 GLN cc_start: 0.7173 (tp40) cc_final: 0.6848 (tm-30) REVERT: E 101 TYR cc_start: 0.8761 (p90) cc_final: 0.8432 (p90) REVERT: B 135 ASN cc_start: 0.6844 (m-40) cc_final: 0.6175 (t0) REVERT: B 233 GLN cc_start: 0.6636 (mm-40) cc_final: 0.6012 (mm-40) REVERT: B 318 LYS cc_start: 0.8761 (tptt) cc_final: 0.8538 (tptp) REVERT: b 62 GLN cc_start: 0.8299 (mp10) cc_final: 0.8091 (mp10) REVERT: D 79 TYR cc_start: 0.8262 (m-80) cc_final: 0.8057 (m-80) REVERT: F 24 ARG cc_start: 0.8018 (ptm-80) cc_final: 0.7595 (ptp-110) REVERT: C 135 ASN cc_start: 0.6800 (m-40) cc_final: 0.6194 (t0) REVERT: C 233 GLN cc_start: 0.6563 (mm-40) cc_final: 0.5973 (mm-40) REVERT: C 318 LYS cc_start: 0.8825 (tptt) cc_final: 0.8593 (tptp) REVERT: c 75 LYS cc_start: 0.8549 (tptt) cc_final: 0.8019 (tttt) REVERT: c 90 ASP cc_start: 0.7777 (m-30) cc_final: 0.7540 (m-30) REVERT: c 149 MET cc_start: 0.7973 (mtm) cc_final: 0.7563 (mtt) outliers start: 30 outliers final: 22 residues processed: 270 average time/residue: 0.1277 time to fit residues: 52.6323 Evaluate side-chains 259 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 236 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 149 MET Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain c residue 38 LEU Chi-restraints excluded: chain c residue 61 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 85 optimal weight: 0.9990 chunk 172 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 154 optimal weight: 0.0050 chunk 128 optimal weight: 5.9990 chunk 147 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 HIS ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN b 124 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 ASN ** c 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.157653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.133008 restraints weight = 22987.669| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.34 r_work: 0.3480 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17823 Z= 0.133 Angle : 0.563 9.902 24216 Z= 0.286 Chirality : 0.044 0.329 2676 Planarity : 0.004 0.045 3087 Dihedral : 5.631 57.548 2877 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.51 % Allowed : 12.63 % Favored : 84.86 % 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: -0.85 (0.18), residues: 2157 helix: 1.98 (0.26), residues: 360 sheet: -1.04 (0.24), residues: 474 loop : -1.14 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 170 TYR 0.014 0.001 TYR D 100 PHE 0.009 0.001 PHE B 105 TRP 0.018 0.001 TRP G 94 HIS 0.002 0.001 HIS C 191 Details of bonding type rmsd covalent geometry : bond 0.00319 (17781) covalent geometry : angle 0.55360 (24108) SS BOND : bond 0.00248 ( 18) SS BOND : angle 0.59397 ( 36) hydrogen bonds : bond 0.03595 ( 570) hydrogen bonds : angle 5.52436 ( 1566) link_BETA1-4 : bond 0.00349 ( 3) link_BETA1-4 : angle 0.92895 ( 9) link_NAG-ASN : bond 0.00298 ( 21) link_NAG-ASN : angle 2.00644 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 244 time to evaluate : 0.689 Fit side-chains REVERT: H 66 ARG cc_start: 0.6676 (mmp-170) cc_final: 0.6423 (mmp80) REVERT: L 24 ARG cc_start: 0.8013 (ptm-80) cc_final: 0.7774 (ptp-110) REVERT: A 135 ASN cc_start: 0.6706 (m-40) cc_final: 0.6224 (t0) REVERT: a 149 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7673 (mtt) REVERT: E 66 ARG cc_start: 0.6798 (mmp-170) cc_final: 0.6380 (mmp80) REVERT: E 101 TYR cc_start: 0.8812 (p90) cc_final: 0.8517 (p90) REVERT: E 101 PHE cc_start: 0.8722 (m-80) cc_final: 0.8514 (m-80) REVERT: B 135 ASN cc_start: 0.6894 (m-40) cc_final: 0.6194 (t0) REVERT: B 318 LYS cc_start: 0.8744 (tptt) cc_final: 0.8518 (tptp) REVERT: b 123 ARG cc_start: 0.8345 (ttp-170) cc_final: 0.8116 (ttp-170) REVERT: b 124 ASN cc_start: 0.7817 (m110) cc_final: 0.7569 (m-40) REVERT: D 79 TYR cc_start: 0.8262 (m-80) cc_final: 0.8018 (m-80) REVERT: D 101 PHE cc_start: 0.8757 (m-80) cc_final: 0.8382 (m-80) REVERT: F 24 ARG cc_start: 0.8033 (ptm-80) cc_final: 0.7627 (ptp-110) REVERT: C 135 ASN cc_start: 0.6771 (m-40) cc_final: 0.6219 (t0) REVERT: C 318 LYS cc_start: 0.8780 (tptt) cc_final: 0.8544 (tptp) REVERT: c 75 LYS cc_start: 0.8547 (tptt) cc_final: 0.8001 (tttt) REVERT: c 90 ASP cc_start: 0.7776 (m-30) cc_final: 0.7545 (m-30) REVERT: c 149 MET cc_start: 0.7968 (mtm) cc_final: 0.7547 (mtt) outliers start: 47 outliers final: 32 residues processed: 272 average time/residue: 0.1240 time to fit residues: 51.9126 Evaluate side-chains 258 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 225 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 149 MET Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain b residue 38 LEU Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain c residue 38 LEU Chi-restraints excluded: chain c residue 61 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 56 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 212 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN A 18 HIS A 303 GLN A 304 ASN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS B 303 GLN b 50 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 50 ASN ** c 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.147240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.122498 restraints weight = 23482.356| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.34 r_work: 0.3347 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.132 17823 Z= 0.298 Angle : 0.722 10.558 24216 Z= 0.368 Chirality : 0.050 0.349 2676 Planarity : 0.005 0.071 3087 Dihedral : 6.271 59.427 2877 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.10 % Allowed : 12.89 % Favored : 84.00 % 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: -1.25 (0.17), residues: 2157 helix: 1.30 (0.26), residues: 357 sheet: -1.23 (0.24), residues: 450 loop : -1.31 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 84 TYR 0.025 0.002 TYR F 91 PHE 0.025 0.003 PHE A 105 TRP 0.036 0.003 TRP B 160 HIS 0.008 0.002 HIS C 191 Details of bonding type rmsd covalent geometry : bond 0.00728 (17781) covalent geometry : angle 0.71128 (24108) SS BOND : bond 0.00509 ( 18) SS BOND : angle 0.98506 ( 36) hydrogen bonds : bond 0.04118 ( 570) hydrogen bonds : angle 6.10100 ( 1566) link_BETA1-4 : bond 0.00576 ( 3) link_BETA1-4 : angle 0.99401 ( 9) link_NAG-ASN : bond 0.00456 ( 21) link_NAG-ASN : angle 2.45123 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 248 time to evaluate : 0.495 Fit side-chains REVERT: A 96 ASP cc_start: 0.7521 (t0) cc_final: 0.7027 (m-30) REVERT: A 135 ASN cc_start: 0.7078 (m-40) cc_final: 0.6282 (t0) REVERT: A 139 ASN cc_start: 0.7728 (OUTLIER) cc_final: 0.7444 (m110) REVERT: a 112 ASP cc_start: 0.8118 (m-30) cc_final: 0.7795 (m-30) REVERT: a 149 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7823 (mtt) REVERT: E 66 ARG cc_start: 0.6964 (mmp-170) cc_final: 0.6139 (mmp80) REVERT: E 101 PHE cc_start: 0.9010 (m-80) cc_final: 0.8787 (m-80) REVERT: B 96 ASP cc_start: 0.7506 (t0) cc_final: 0.7084 (m-30) REVERT: B 135 ASN cc_start: 0.7304 (m-40) cc_final: 0.6231 (t0) REVERT: D 79 TYR cc_start: 0.8488 (m-80) cc_final: 0.8196 (m-80) REVERT: D 101 TYR cc_start: 0.8831 (p90) cc_final: 0.8490 (p90) REVERT: D 101 PHE cc_start: 0.9013 (m-80) cc_final: 0.8503 (m-80) REVERT: C 135 ASN cc_start: 0.7262 (m-40) cc_final: 0.6448 (t0) REVERT: C 318 LYS cc_start: 0.8900 (tptt) cc_final: 0.8685 (tptp) REVERT: c 75 LYS cc_start: 0.8705 (tptt) cc_final: 0.8182 (tttt) REVERT: c 90 ASP cc_start: 0.7934 (m-30) cc_final: 0.7718 (m-30) outliers start: 58 outliers final: 42 residues processed: 285 average time/residue: 0.1393 time to fit residues: 59.0982 Evaluate side-chains 271 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 227 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 149 MET Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain b residue 38 LEU Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain c residue 38 LEU Chi-restraints excluded: chain c residue 49 THR Chi-restraints excluded: chain c residue 61 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 10 optimal weight: 0.5980 chunk 210 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 205 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 55 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: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN A 18 HIS A 304 ASN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS ** c 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.151650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.127082 restraints weight = 23240.369| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.33 r_work: 0.3401 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17823 Z= 0.153 Angle : 0.606 10.101 24216 Z= 0.307 Chirality : 0.046 0.340 2676 Planarity : 0.004 0.052 3087 Dihedral : 6.055 58.581 2877 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.51 % Allowed : 13.75 % Favored : 83.73 % 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: -1.01 (0.18), residues: 2157 helix: 1.58 (0.26), residues: 360 sheet: -1.08 (0.24), residues: 474 loop : -1.17 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 66 TYR 0.021 0.002 TYR E 100 PHE 0.011 0.002 PHE F 71 TRP 0.022 0.002 TRP B 160 HIS 0.003 0.001 HIS A 191 Details of bonding type rmsd covalent geometry : bond 0.00368 (17781) covalent geometry : angle 0.59664 (24108) SS BOND : bond 0.00293 ( 18) SS BOND : angle 0.62993 ( 36) hydrogen bonds : bond 0.03705 ( 570) hydrogen bonds : angle 5.82091 ( 1566) link_BETA1-4 : bond 0.00246 ( 3) link_BETA1-4 : angle 1.03617 ( 9) link_NAG-ASN : bond 0.00362 ( 21) link_NAG-ASN : angle 2.16269 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 253 time to evaluate : 0.627 Fit side-chains REVERT: H 66 ARG cc_start: 0.6840 (mmp-170) cc_final: 0.6596 (mmp80) REVERT: A 96 ASP cc_start: 0.7478 (t0) cc_final: 0.6986 (m-30) REVERT: A 135 ASN cc_start: 0.6992 (m-40) cc_final: 0.6232 (t0) REVERT: A 318 LYS cc_start: 0.8762 (tptt) cc_final: 0.8506 (tptp) REVERT: a 97 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8153 (mm-30) REVERT: a 112 ASP cc_start: 0.8045 (m-30) cc_final: 0.7711 (m-30) REVERT: a 149 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7711 (mtt) REVERT: E 49 SER cc_start: 0.8170 (m) cc_final: 0.7930 (t) REVERT: E 66 ARG cc_start: 0.6883 (OUTLIER) cc_final: 0.6023 (mmp80) REVERT: B 96 ASP cc_start: 0.7441 (t0) cc_final: 0.7009 (m-30) REVERT: B 135 ASN cc_start: 0.7167 (m-40) cc_final: 0.6145 (t0) REVERT: B 173 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7535 (mm-40) REVERT: b 17 MET cc_start: 0.8392 (mtt) cc_final: 0.8015 (mtt) REVERT: b 112 ASP cc_start: 0.8063 (m-30) cc_final: 0.7760 (m-30) REVERT: D 79 TYR cc_start: 0.8436 (m-80) cc_final: 0.8140 (m-80) REVERT: D 101 PHE cc_start: 0.8892 (m-10) cc_final: 0.8480 (m-80) REVERT: F 93 ASN cc_start: 0.7452 (OUTLIER) cc_final: 0.7192 (t0) REVERT: C 96 ASP cc_start: 0.7398 (t0) cc_final: 0.6956 (m-30) REVERT: C 135 ASN cc_start: 0.7138 (m-40) cc_final: 0.6350 (t0) REVERT: C 224 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7875 (mt) REVERT: C 318 LYS cc_start: 0.8829 (tptt) cc_final: 0.8608 (tptp) REVERT: c 75 LYS cc_start: 0.8599 (tptt) cc_final: 0.8018 (tttt) REVERT: c 90 ASP cc_start: 0.7831 (m-30) cc_final: 0.7589 (m-30) outliers start: 47 outliers final: 37 residues processed: 283 average time/residue: 0.1305 time to fit residues: 55.7125 Evaluate side-chains 269 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 228 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 149 MET Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain c residue 38 LEU Chi-restraints excluded: chain c residue 61 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 147 optimal weight: 0.9980 chunk 194 optimal weight: 0.0870 chunk 22 optimal weight: 3.9990 chunk 181 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 69 optimal weight: 0.0040 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.5770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 HIS ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 124 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.153663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.129012 restraints weight = 23153.999| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.34 r_work: 0.3428 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17823 Z= 0.132 Angle : 0.586 10.116 24216 Z= 0.297 Chirality : 0.045 0.318 2676 Planarity : 0.004 0.053 3087 Dihedral : 5.888 57.342 2877 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.62 % Allowed : 13.59 % Favored : 83.79 % 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: -0.82 (0.18), residues: 2157 helix: 1.83 (0.26), residues: 360 sheet: -0.89 (0.25), residues: 468 loop : -1.11 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG b 170 TYR 0.022 0.002 TYR D 100 PHE 0.011 0.001 PHE F 71 TRP 0.022 0.002 TRP L 94 HIS 0.003 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00315 (17781) covalent geometry : angle 0.57731 (24108) SS BOND : bond 0.00260 ( 18) SS BOND : angle 0.58486 ( 36) hydrogen bonds : bond 0.03584 ( 570) hydrogen bonds : angle 5.65716 ( 1566) link_BETA1-4 : bond 0.00384 ( 3) link_BETA1-4 : angle 1.09262 ( 9) link_NAG-ASN : bond 0.00325 ( 21) link_NAG-ASN : angle 2.04505 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 244 time to evaluate : 0.538 Fit side-chains REVERT: A 96 ASP cc_start: 0.7468 (t0) cc_final: 0.6989 (m-30) REVERT: A 135 ASN cc_start: 0.6973 (m-40) cc_final: 0.6243 (t0) REVERT: A 318 LYS cc_start: 0.8757 (tptt) cc_final: 0.8506 (tptp) REVERT: a 17 MET cc_start: 0.8113 (mtt) cc_final: 0.7864 (mtt) REVERT: a 97 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8037 (mm-30) REVERT: a 149 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7678 (mtt) REVERT: E 49 SER cc_start: 0.8086 (m) cc_final: 0.7879 (t) REVERT: E 101 PHE cc_start: 0.8874 (m-80) cc_final: 0.8405 (m-80) REVERT: B 96 ASP cc_start: 0.7442 (t0) cc_final: 0.7018 (m-30) REVERT: B 135 ASN cc_start: 0.7075 (m-40) cc_final: 0.6196 (t0) REVERT: B 173 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7543 (mm-40) REVERT: b 27 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7361 (tt0) REVERT: b 112 ASP cc_start: 0.8084 (m-30) cc_final: 0.7721 (m-30) REVERT: D 79 TYR cc_start: 0.8410 (m-80) cc_final: 0.8117 (m-80) REVERT: D 101 PHE cc_start: 0.8771 (m-10) cc_final: 0.8546 (m-80) REVERT: C 96 ASP cc_start: 0.7379 (t0) cc_final: 0.6950 (m-30) REVERT: C 135 ASN cc_start: 0.7077 (m-40) cc_final: 0.6304 (t0) REVERT: C 224 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7841 (mt) REVERT: C 318 LYS cc_start: 0.8843 (tptt) cc_final: 0.8628 (tptp) REVERT: c 75 LYS cc_start: 0.8591 (tptt) cc_final: 0.8000 (tttt) outliers start: 49 outliers final: 36 residues processed: 275 average time/residue: 0.1251 time to fit residues: 52.3794 Evaluate side-chains 277 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 238 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 149 MET Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain b residue 27 GLN Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain c residue 38 LEU Chi-restraints excluded: chain c residue 61 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 169 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 168 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.151218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126550 restraints weight = 23248.721| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.32 r_work: 0.3390 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 17823 Z= 0.186 Angle : 0.624 10.117 24216 Z= 0.316 Chirality : 0.046 0.315 2676 Planarity : 0.004 0.047 3087 Dihedral : 5.971 58.608 2877 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.57 % Allowed : 13.70 % Favored : 83.73 % 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: -0.87 (0.18), residues: 2157 helix: 1.71 (0.26), residues: 360 sheet: -0.88 (0.25), residues: 468 loop : -1.14 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG c 170 TYR 0.022 0.002 TYR H 91 PHE 0.014 0.002 PHE B 105 TRP 0.023 0.002 TRP A 160 HIS 0.007 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00453 (17781) covalent geometry : angle 0.61466 (24108) SS BOND : bond 0.00350 ( 18) SS BOND : angle 0.71944 ( 36) hydrogen bonds : bond 0.03629 ( 570) hydrogen bonds : angle 5.74022 ( 1566) link_BETA1-4 : bond 0.00264 ( 3) link_BETA1-4 : angle 0.98892 ( 9) link_NAG-ASN : bond 0.00356 ( 21) link_NAG-ASN : angle 2.14493 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 237 time to evaluate : 0.582 Fit side-chains REVERT: A 96 ASP cc_start: 0.7501 (t0) cc_final: 0.6982 (m-30) REVERT: A 135 ASN cc_start: 0.7042 (m-40) cc_final: 0.6253 (t0) REVERT: a 97 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7981 (mm-30) REVERT: a 149 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7703 (mtt) REVERT: E 101 TYR cc_start: 0.8865 (p90) cc_final: 0.8637 (p90) REVERT: E 101 PHE cc_start: 0.8809 (m-80) cc_final: 0.8528 (m-80) REVERT: B 96 ASP cc_start: 0.7430 (t0) cc_final: 0.7038 (m-30) REVERT: B 135 ASN cc_start: 0.7196 (m-40) cc_final: 0.6188 (t0) REVERT: B 173 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7504 (mm-40) REVERT: b 27 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7446 (tt0) REVERT: D 79 TYR cc_start: 0.8454 (m-80) cc_final: 0.8144 (m-80) REVERT: D 101 PHE cc_start: 0.8790 (m-10) cc_final: 0.8466 (m-80) REVERT: C 96 ASP cc_start: 0.7396 (t0) cc_final: 0.6942 (m-30) REVERT: C 135 ASN cc_start: 0.7136 (m-40) cc_final: 0.6335 (t0) REVERT: C 318 LYS cc_start: 0.8823 (tptt) cc_final: 0.8601 (tptp) REVERT: c 75 LYS cc_start: 0.8586 (tptt) cc_final: 0.7986 (tttt) outliers start: 48 outliers final: 44 residues processed: 268 average time/residue: 0.1260 time to fit residues: 51.2235 Evaluate side-chains 270 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 224 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 149 MET Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain b residue 27 GLN Chi-restraints excluded: chain b residue 38 LEU Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain c residue 38 LEU Chi-restraints excluded: chain c residue 61 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 58 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 4 optimal weight: 0.0970 chunk 182 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.161762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.136994 restraints weight = 23302.470| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.22 r_work: 0.3482 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 17823 Z= 0.187 Angle : 0.630 10.258 24216 Z= 0.319 Chirality : 0.046 0.314 2676 Planarity : 0.004 0.046 3087 Dihedral : 6.025 58.970 2877 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.57 % Allowed : 14.13 % Favored : 83.31 % 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: -0.90 (0.18), residues: 2157 helix: 1.67 (0.26), residues: 360 sheet: -0.89 (0.25), residues: 468 loop : -1.15 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 66 TYR 0.022 0.002 TYR G 91 PHE 0.013 0.002 PHE B 105 TRP 0.022 0.002 TRP A 160 HIS 0.006 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00455 (17781) covalent geometry : angle 0.62110 (24108) SS BOND : bond 0.00344 ( 18) SS BOND : angle 0.73514 ( 36) hydrogen bonds : bond 0.03659 ( 570) hydrogen bonds : angle 5.76467 ( 1566) link_BETA1-4 : bond 0.00202 ( 3) link_BETA1-4 : angle 1.01779 ( 9) link_NAG-ASN : bond 0.00358 ( 21) link_NAG-ASN : angle 2.13844 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 237 time to evaluate : 0.640 Fit side-chains REVERT: A 96 ASP cc_start: 0.7515 (t0) cc_final: 0.7062 (m-30) REVERT: A 135 ASN cc_start: 0.7041 (m-40) cc_final: 0.6262 (t0) REVERT: a 97 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7996 (mm-30) REVERT: a 149 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7695 (mtt) REVERT: E 90 VAL cc_start: 0.8175 (p) cc_final: 0.7952 (p) REVERT: E 101 TYR cc_start: 0.8868 (p90) cc_final: 0.8631 (p90) REVERT: E 101 PHE cc_start: 0.8884 (m-80) cc_final: 0.8581 (m-80) REVERT: B 96 ASP cc_start: 0.7473 (t0) cc_final: 0.7115 (m-30) REVERT: B 135 ASN cc_start: 0.7186 (m-40) cc_final: 0.6213 (t0) REVERT: B 173 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7585 (mm-40) REVERT: b 27 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7466 (tt0) REVERT: D 79 TYR cc_start: 0.8515 (m-80) cc_final: 0.8266 (m-80) REVERT: D 101 PHE cc_start: 0.8847 (m-10) cc_final: 0.8522 (m-80) REVERT: F 91 TYR cc_start: 0.7385 (t80) cc_final: 0.7173 (t80) REVERT: C 96 ASP cc_start: 0.7388 (t0) cc_final: 0.7004 (m-30) REVERT: C 135 ASN cc_start: 0.7152 (m-40) cc_final: 0.6401 (t0) REVERT: c 75 LYS cc_start: 0.8669 (tptt) cc_final: 0.8098 (tttt) outliers start: 48 outliers final: 44 residues processed: 269 average time/residue: 0.1339 time to fit residues: 53.9348 Evaluate side-chains 273 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 227 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 149 MET Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain b residue 27 GLN Chi-restraints excluded: chain b residue 38 LEU Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain c residue 38 LEU Chi-restraints excluded: chain c residue 61 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 127 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 193 optimal weight: 0.6980 chunk 149 optimal weight: 0.1980 chunk 103 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.161786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.136998 restraints weight = 23389.493| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.23 r_work: 0.3495 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17823 Z= 0.181 Angle : 0.629 10.246 24216 Z= 0.318 Chirality : 0.046 0.309 2676 Planarity : 0.004 0.046 3087 Dihedral : 6.028 59.117 2877 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.73 % Allowed : 14.29 % Favored : 82.99 % 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: -0.87 (0.18), residues: 2157 helix: 1.69 (0.26), residues: 360 sheet: -0.86 (0.25), residues: 468 loop : -1.14 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG c 170 TYR 0.022 0.002 TYR E 100 PHE 0.013 0.002 PHE C 105 TRP 0.021 0.002 TRP A 160 HIS 0.006 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00441 (17781) covalent geometry : angle 0.61964 (24108) SS BOND : bond 0.00334 ( 18) SS BOND : angle 0.70820 ( 36) hydrogen bonds : bond 0.03643 ( 570) hydrogen bonds : angle 5.75595 ( 1566) link_BETA1-4 : bond 0.00259 ( 3) link_BETA1-4 : angle 1.05683 ( 9) link_NAG-ASN : bond 0.00366 ( 21) link_NAG-ASN : angle 2.12541 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4397.34 seconds wall clock time: 76 minutes 16.46 seconds (4576.46 seconds total)